Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/v/vg/vg_1.30.0+ds-1_all.buildinfo
Use metasnap for getting required timestamps
New buildinfo file: /tmp/vg-1.30.0+ds-1phf0jlws/vg_1.30.0+ds-1_all.buildinfo
Get source package info: vg=1.30.0+ds-1
Source URL: http://snapshot.notset.fr/mr/package/vg/1.30.0+ds-1/srcfiles?fileinfo=1
env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-3 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-2 bc=1.07.1-2+b2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bison=2:3.7.4+dfsg-1 bsdextrautils=2.36.1-6 bsdmainutils=12.1.7 bsdutils=1:2.36.1-6 build-essential=12.9 bwa=0.7.17-5 bzip2=1.0.8-4 ca-certificates=20210119 calendar=12.1.7 cmake=3.18.4-1+b1 cmake-data=3.18.4-1 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.10.0-1 diffutils=1:3.7-5 docbook=4.5-6 docbook-to-man=1:2.0.0-45 docbook-xml=4.5-9 docbook-xsl=1.79.2+dfsg-1 doxygen=1.9.1-1 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20210118-1 elfutils=0.182-3 fastahack=1.0.0+dfsg-7 file=1:5.39-3 findutils=4.8.0-1 flex=2.6.4-8 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.1-1 g++-10=10.2.1-6 gawk=1:5.0.1+dfsg-1 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-3 gettext-base=0.21-3 graphviz=2.42.2-4+b2 grep=3.6-1 groff-base=1.22.4-6 gtk-doc-tools=1.33.1-1 gzip=1.10-2 help2man=1.47.17 hostname=3.23 icu-devtools=67.1-6 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 jq=1.6-2.1 libacl1=2.2.53-9 libann0=1.1.2+doc-7 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2 libasan6=10.2.1-6 libasm1=0.182-3 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbackward-cpp-dev=1.5-2 libbinutils=2.35.1-7 libblas3=3.9.0-3 libblkid-dev=2.36.1-6 libblkid1=2.36.1-6 libboost-program-options-dev=1.74.0.3 libboost-program-options1.74-dev=1.74.0-8 libboost-program-options1.74.0=1.74.0-8 libboost1.74-dev=1.74.0-8 libbrotli-dev=1.0.9-2+b2 libbrotli1=1.0.9-2+b2 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcairo-gobject2=1.16.0-5 libcairo-script-interpreter2=1.16.0-5 libcairo2=1.16.0-5 libcairo2-dev=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcdt5=2.42.2-4+b2 libcgraph6=2.42.2-4+b2 libclang-cpp11=1:11.0.1-2 libclang1-11=1:11.0.1-2 libcom-err2=1.45.6-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libcurl3-gnutls=7.74.0-1 libcurl4=7.74.0-1 libcurl4-gnutls-dev=7.74.0-1 libdatrie1=0.2.12-3 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.256 libdebhelper-perl=13.3.1 libdeflate-dev=1.7-1 libdeflate0=1.7-1 libdisorder-dev=0.0.2+git20130809.8062ee1-2 libdisorder0=0.0.2+git20130809.8062ee1-2 libdivsufsort-dev=2.0.1-5 libdivsufsort3=2.0.1-5 libdpkg-perl=1.20.7.1 libdw-dev=0.182-3 libdw1=0.182-3 libedit2=3.1-20191231-2+b1 libelf-dev=0.182-3 libelf1=0.182-3 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libfastahack-dev=1.0.0+dfsg-7 libfastahack0=1.0.0+dfsg-7 libffi-dev=3.3-5 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.10.0-1 libfml-dev=0.1+git20190320.b499514-1+b1 libfml0=0.1+git20190320.b499514-1+b1 libfontconfig-dev=2.13.1-4.2 libfontconfig1=2.13.1-4.2 libfontconfig1-dev=2.13.1-4.2 libfreetype-dev=2.10.4+dfsg-1 libfreetype6=2.10.4+dfsg-1 libfreetype6-dev=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-2 libgd3=2.3.0-2 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgfortran5=10.2.1-6 libglib2.0-0=2.66.4-1 libglib2.0-bin=2.66.4-1 libglib2.0-data=2.66.4-1 libglib2.0-dev=2.66.4-1 libglib2.0-dev-bin=2.66.4-1 libgmp-dev=2:6.2.1+dfsg-1 libgmp10=2:6.2.1+dfsg-1 libgmpxx4ldbl=2:6.2.1+dfsg-1 libgnutls30=3.7.0-5 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-4 libgts-0.7-5=0.7.6+darcs121130-4+b1 libgvc6=2.42.2-4+b2 libgvpr2=2.42.2-4+b2 libharfbuzz0b=2.7.4-1 libhogweed6=3.6-2 libhts-dev=1.11-4 libhts3=1.11-4 libice-dev=2:1.0.10-1 libice6=2:1.0.10-1 libicu-dev=67.1-6 libicu67=67.1-6 libidn2-0=2.3.0-5 libisl23=0.23-1 libitm1=10.2.1-6 libjansson-dev=2.13.1-1 libjansson4=2.13.1-1 libjbig0=2.1-3.1+b2 libjemalloc-dev=5.2.1-2 libjemalloc2=5.2.1-2 libjpeg62-turbo=1:2.0.5-2 libjq1=1.6-2.1 libjsoncpp24=1.9.4-4 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblab-gamut1=2.42.2-4+b2 liblapack3=3.9.0-3 libldap-2.4-2=2.4.57+dfsg-1 libllvm11=1:11.0.1-2 liblocale-gettext-perl=1.07-4+b1 liblsan0=10.2.1-6 libltdl7=2.4.6-15 liblz4-1=1.9.3-1 liblz4-dev=1.9.3-1 liblzma-dev=5.2.5-1.0 liblzma5=5.2.5-1.0 liblzo2-2=2.10-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmhash2=0.9.9.9-9 libmount-dev=2.36.1-6 libmount1=2.36.1-6 libmpc3=1.2.0-1 libmpdec3=2.5.1~rc1-2 libmpfr6=4.1.0-3 libncurses-dev=6.2+20201114-2 libncurses5-dev=6.2+20201114-2 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnettle8=3.6-2 libnghttp2-14=1.42.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libonig5=6.9.5-2 libosp5=1.5.2-13+b2 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-2 libpam-modules-bin=1.4.0-2 libpam-runtime=1.4.0-2 libpam0g=1.4.0-2 libpango-1.0-0=1.46.2-3 libpangocairo-1.0-0=1.46.2-3 libpangoft2-1.0-0=1.46.2-3 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpathplan4=2.42.2-4+b2 libpcre16-3=2:8.39-13 libpcre2-16-0=10.36-2 libpcre2-32-0=10.36-2 libpcre2-8-0=10.36-2 libpcre2-dev=10.36-2 libpcre2-posix2=10.36-2 libpcre3=2:8.39-13 libpcre3-dev=2:8.39-13 libpcre32-3=2:8.39-13 libpcrecpp0v5=2:8.39-13 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpixman-1-dev=0.40.0-1 libpng-dev=1.6.37-3 libpng16-16=1.6.37-3 libprocps8=2:3.3.16-5 libprotobuf-dev=3.12.4-1 libprotobuf-lite23=3.12.4-1 libprotobuf23=3.12.4-1 libprotoc-dev=3.12.4-1 libprotoc23=3.12.4-1 libpsl5=0.21.0-1.1 libpthread-stubs0-dev=0.4-1 libpython3-stdlib=3.9.1-1 libpython3.9-minimal=3.9.1-3 libpython3.9-stdlib=3.9.1-3 libquadmath0=10.2.1-6 libraptor2-0=2.0.14-1.2 libraptor2-dev=2.0.14-1.2 librasqal3=0.9.33-0.1 librasqal3-dev=0.9.33-0.1 librdf0=1.0.17-1.1+b1 librdf0-dev=1.0.17-1.1+b1 libreadline8=8.1-1 librhash0=1.4.1-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libselinux1-dev=3.1-2+b2 libsepol1=3.1-1 libsepol1-dev=3.1-1 libsigsegv2=2.12-3 libsimde-dev=0.7.2-3 libsm-dev=2:1.2.3-1 libsm6=2:1.2.3-1 libsmartcols1=2.36.1-6 libsmithwaterman-dev=0.0+git20160702.2610e25-11 libsmithwaterman0=0.0+git20160702.2610e25-11 libsparsehash-dev=2.0.3-2 libsqlite3-0=3.34.1-1 libssh2-1=1.9.0-2 libssl1.1=1.1.1i-2 libssw-dev=1.1-12+b1 libssw0=1.1-12+b1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.2-5 libtabixpp-dev=1.1.0-3 libtabixpp0=1.1.0-3 libtasn1-6=4.16.0-2 libtcl8.6=8.6.11+dfsg-1 libthai-data=0.1.28-3 libthai0=0.1.28-3 libtiff5=4.2.0-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtk8.6=8.6.11-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libtsl-hopscotch-map-dev=2.3.0-1 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.2-5 libunistring2=0.9.10-4 libuuid1=2.36.1-6 libuv1=1.40.0-1 libvcflib-dev=1.0.1+dfsg-4 libvcflib-tools=1.0.1+dfsg-4 libvcflib1=1.0.1+dfsg-4 libwebp6=0.6.1-2+b1 libx11-6=2:1.7.0-2 libx11-data=2:1.7.0-2 libx11-dev=2:1.7.0-2 libxapian30=1.4.18-1 libxau-dev=1:1.0.8-1+b2 libxau6=1:1.0.8-1+b2 libxaw7=2:1.0.13-1.1 libxcb-render0=1.14-2.1 libxcb-render0-dev=1.14-2.1 libxcb-shm0=1.14-2.1 libxcb-shm0-dev=1.14-2.1 libxcb1=1.14-2.1 libxcb1-dev=1.14-2.1 libxdmcp-dev=1:1.1.2-3 libxdmcp6=1:1.1.2-3 libxext-dev=2:1.3.3-1.1 libxext6=2:1.3.3-1.1 libxft2=2.3.2-2 libxml2=2.9.10+dfsg-6.3+b1 libxml2-dev=2.9.10+dfsg-6.3+b1 libxmu6=2:1.1.2-2+b3 libxpm4=1:3.5.12-1 libxrender-dev=1:0.9.10-1 libxrender1=1:0.9.10-1 libxslt1-dev=1.1.34-4 libxslt1.1=1.1.34-4 libxss1=1:1.2.3-1 libxt6=1:1.2.0-1 libyajl-dev=2.1.0-3 libyajl2=2.1.0-3 libz3-4=4.8.9-1 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.10.9-1 littler=0.3.12-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.68 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncal=12.1.7 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 opensp=1.5.2-13+b2 openssl=1.1.1i-2 patch=2.7.6-7 perl=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 procps=2:3.3.16-5 protobuf-compiler=3.12.4-1 pv=1.6.6-1+b1 python3=3.9.1-1 python3-distutils=3.9.1-2 python3-lib2to3=3.9.1-2 python3-lxml=4.6.2-1 python3-minimal=3.9.1-1 python3-pkg-resources=51.3.3-1 python3-pygments=2.7.1+dfsg-1 python3.9=3.9.1-3 python3.9-minimal=3.9.1-3 r-base-core=4.0.3-1 r-cran-assertthat=0.2.1-2 r-cran-brio=1.1.1-1 r-cran-callr=3.5.1-1 r-cran-cli=2.2.0-1 r-cran-colorspace=2.0-0+dfsg-1 r-cran-crayon=1.3.4-5 r-cran-desc=1.2.0-3 r-cran-diffobj=0.3.2-1 r-cran-digest=0.6.27-1 r-cran-ellipsis=0.3.1-1 r-cran-evaluate=0.14-2 r-cran-fansi=0.4.2-1 r-cran-farver=2.0.3-1+b1 r-cran-ggplot2=3.3.3+dfsg-1 r-cran-glue=1.4.2-1 r-cran-gridbase=0.4-7-5 r-cran-gtable=0.3.0+dfsg-2 r-cran-isoband=0.2.3-2 r-cran-jsonlite=1.7.2+dfsg-1 r-cran-labeling=0.4.2-1 r-cran-lattice=0.20-41-1+b1 r-cran-lifecycle=0.2.0-2 r-cran-littler=0.3.12-1 r-cran-magrittr=2.0.1-1 r-cran-mass=7.3-53-1 r-cran-matrix=1.3-2-1 r-cran-mgcv=1.8-33-1 r-cran-munsell=0.5.0-2 r-cran-nlme=3.1.151-1 r-cran-pillar=1.4.7-1 r-cran-pkgbuild=1.2.0-1 r-cran-pkgconfig=2.0.3-2 r-cran-pkgkitten=0.2.0-1 r-cran-pkgload=1.1.0-1 r-cran-plyr=1.8.6-2 r-cran-praise=1.0.0-4 r-cran-prettyunits=1.1.1-2 r-cran-processx=3.4.5-1 r-cran-ps=1.5.0-1 r-cran-r6=2.5.0-1 r-cran-rcolorbrewer=1.1-2-3 r-cran-rcpp=1.0.6-1 r-cran-rematch2=2.1.2-2 r-cran-rlang=0.4.10-1 r-cran-rprojroot=2.0.2-1 r-cran-rstudioapi=0.13-1 r-cran-scales=1.1.1-1 r-cran-testthat=3.0.1-1 r-cran-tibble=3.0.5+dfsg-1 r-cran-utf8=1.1.4-2 r-cran-vctrs=0.3.6-1 r-cran-viridislite=0.3.0-4 r-cran-waldo=0.2.3-2 r-cran-withr=2.4.0-1 rapidjson-dev=1.1.0+dfsg2-7 raptor2-utils=2.0.14-1.2 rasqal-utils=0.9.33-0.1 readline-common=8.1-1 rs=20200313-1 samtools=1.11-1 sed=4.7-1 sensible-utils=0.0.14 sgml-base=1.30 sgml-data=2.0.11+nmu1 sysvinit-utils=2.96-5 tabix=1.11-4 tar=1.32+dfsg-1 tzdata=2020f-1 ucf=3.0043 unzip=6.0-26 util-linux=2.36.1-6 uuid-dev=2.36.1-6 x11-common=1:7.7+21 x11proto-core-dev=2020.1-1 x11proto-dev=2020.1-1 x11proto-xext-dev=2020.1-1 xdg-utils=1.1.3-4 xml-core=0.18+nmu1 xorg-sgml-doctools=1:1.11-1.1 xsltproc=1.1.34-4 xtrans-dev=1.4.0-1 xxd=2:8.2.2367-1 xz-utils=5.2.5-1.0 zip=3.0-11+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main
deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main
deb http://snapshot.notset.fr/archive/debian/20210129T152007Z/ unstable main
deb http://snapshot.notset.fr/archive/debian/20210124T203726Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d vg=1.30.0+ds-1 && mkdir -p /build/vg-t08NLS && dpkg-source --no-check -x /*.dsc /build/vg-t08NLS/vg-1.30.0+ds && chown -R builduser:builduser /build/vg-t08NLS" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/vg-t08NLS/vg-1.30.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1611746912" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/vg-t08NLS /tmp/vg-1.30.0+ds-1phf0jlws bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210124T203726Z unstable main
I: automatically chosen mode: root
I: chroot architecture amd64 is equal to the host's architecture
I: automatically chosen format: tar
I: using /tmp/mmdebstrap.Jvh0JejnHy as tempdir
I: running apt-get update...
I: downloading packages with apt...
I: extracting archives...
I: installing essential packages...
I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.Jvh0JejnHy
Reading package lists...
Building dependency tree...
util-linux is already the newest version (2.36.1-6).
The following NEW packages will be installed:
  fakeroot libfakeroot
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 134 kB of archives.
After this operation, 397 kB of additional disk space will be used.
Get:1 http://snapshot.notset.fr/archive/debian/20210124T203726Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB]
Get:2 http://snapshot.notset.fr/archive/debian/20210124T203726Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 134 kB in 0s (1086 kB/s)
Selecting previously unselected package libfakeroot:amd64.
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Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ...
Unpacking libfakeroot:amd64 (1.25.3-1.1) ...
Selecting previously unselected package fakeroot.
Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ...
Unpacking fakeroot (1.25.3-1.1) ...
Setting up libfakeroot:amd64 (1.25.3-1.1) ...
Setting up fakeroot (1.25.3-1.1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Processing triggers for libc-bin (2.31-9) ...
I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/
I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main
deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main
deb http://snapshot.notset.fr/archive/debian/20210129T152007Z/ unstable main
deb http://snapshot.notset.fr/archive/debian/20210124T203726Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.Jvh0JejnHy
Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB]
Get:2 http://snapshot.notset.fr/archive/debian/20210129T152007Z unstable InRelease [153 kB]
Hit:3 http://snapshot.notset.fr/archive/debian/20210124T203726Z unstable InRelease
Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources
Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages
Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources
Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages
Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources
Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages
Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB]
Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB]
Ign:6 http://snapshot.notset.fr/archive/debian/20210129T152007Z unstable/main amd64 Packages
Ign:6 http://snapshot.notset.fr/archive/debian/20210129T152007Z unstable/main amd64 Packages
Ign:6 http://snapshot.notset.fr/archive/debian/20210129T152007Z unstable/main amd64 Packages
Get:6 http://snapshot.notset.fr/archive/debian/20210129T152007Z unstable/main amd64 Packages [11.7 MB]
Fetched 34.4 MB in 29s (1172 kB/s)
Reading package lists...
I: installing remaining packages inside the chroot...
I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.Jvh0JejnHy
I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d vg=1.30.0+ds-1 && mkdir -p /build/vg-t08NLS && dpkg-source --no-check -x /*.dsc /build/vg-t08NLS/vg-1.30.0+ds && chown -R builduser:builduser /build/vg-t08NLS"' exec /tmp/mmdebstrap.Jvh0JejnHy
Reading package lists...
NOTICE: 'vg' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/vg.git
Please use:
git clone https://salsa.debian.org/med-team/vg.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 95.1 MB of source archives.
Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (dsc) [2979 B]
Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (tar) [95.0 MB]
Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (diff) [114 kB]
Fetched 95.1 MB in 1min 21s (1178 kB/s)
Download complete and in download only mode
W: Download is performed unsandboxed as root as file 'vg_1.30.0+ds-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied)
dpkg-source: info: extracting vg in /build/vg-t08NLS/vg-1.30.0+ds
dpkg-source: info: unpacking vg_1.30.0+ds.orig.tar.xz
dpkg-source: info: unpacking vg_1.30.0+ds-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying gcc-10
dpkg-source: info: applying use_packaged_libdeflate
dpkg-source: info: applying use_packaged_jemalloc
dpkg-source: info: applying use_packaged_libbackward-cpp
dpkg-source: info: applying use_packaged_elfutils
dpkg-source: info: applying use_packaged_raptor2
dpkg-source: info: applying no_need_for_snappy
dpkg-source: info: applying use_packaged_sparsehash
dpkg-source: info: applying use_packaged_ssw
dpkg-source: info: applying use_packaged_rapidjson
dpkg-source: info: applying use_packaged_fermi-lite
dpkg-source: info: applying spelling
dpkg-source: info: applying no_rpath
dpkg-source: info: applying no_pg
dpkg-source: info: applying use_packaged_fastahack
dpkg-source: info: applying hardening_flags
dpkg-source: info: applying use_packaged_smithwaterman
dpkg-source: info: applying static
dpkg-source: info: applying use_packaged_lz4
dpkg-source: info: applying parallize_better
dpkg-source: info: applying use_packaged_libtsl-hopscotch-map-dev
dpkg-source: info: applying libVCFH_unneeded
dpkg-source: info: applying better_clean
dpkg-source: info: applying use_packaged_vcflib
dpkg-source: info: applying use_packaged_htslib
dpkg-source: info: applying simde
dpkg-source: info: applying crossbuild
dpkg-source: info: applying python3
dpkg-source: info: applying fix-handlegraph
I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/vg-t08NLS/vg-1.30.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1611746912" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.Jvh0JejnHy
dpkg-buildpackage: info: source package vg
dpkg-buildpackage: info: source version 1.30.0+ds-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@debian.org>
 dpkg-source --before-build .
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds'
find /build/vg-t08NLS/vg-1.30.0+ds/include/ -type f -a '!' -name vg_git_version.hpp -delete
dh_auto_clean || true
	make -j4 clean
make[2]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds'
rm -f -r lib
rm -f -r obj/unittest
rm -f -r obj/subcommand
rm -f -r obj/io
rm -f -r obj/algorithms
rm -f -r obj
rm -f -r share/
cd ./deps && cd sonLib && make clean
make[3]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/sonLib'
cd C && make clean
cd externalTools && make clean
make[4]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/sonLib/C'
make[4]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/sonLib/externalTools'
cd cutest && make clean
cd quicktree_1.1 && make clean
rm -rf  ../bin ../lib
make[4]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/sonLib/C'
make[5]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/sonLib/externalTools/cutest'
make[5]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1'
rm -rf ./obj/*.o
rm -f ../../lib/cuTest.a ../../lib/CuTest.h
make[5]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1'
make[5]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/sonLib/externalTools/cutest'
make[4]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/sonLib/externalTools'
rm -f ./bin/sonLib_daemonize.py
make[3]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/sonLib'
cd ./deps && cd gcsa2 && make clean
make[3]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/gcsa2'
Makefile:2: ../sdsl-lite/Make.helper: No such file or directory
make[3]: *** No rule to make target '../sdsl-lite/Make.helper'.  Stop.
make[3]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds/deps/gcsa2'
make[2]: *** [Makefile:691: clean] Error 2
make[2]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds'
dh_auto_clean: error: make -j4 clean returned exit code 2
make[1]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds'
   debian/rules override_dh_clean
make[1]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds'
rm -Rf ./deps/DYNAMIC/build/CMakeFiles
dh_clean
make[1]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds'
 debian/rules binary-indep
dh binary-indep
   dh_update_autotools_config -i
   debian/rules override_dh_autoreconf
make[1]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds'
dh_autoreconf --sourcedirectory=/build/vg-t08NLS/vg-1.30.0+ds/deps/vowpal_wabbit
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'.
libtoolize: copying file 'acinclude.d/libtool.m4'
libtoolize: copying file 'acinclude.d/ltoptions.m4'
libtoolize: copying file 'acinclude.d/ltsugar.m4'
libtoolize: copying file 'acinclude.d/ltversion.m4'
libtoolize: copying file 'acinclude.d/lt~obsolete.m4'
configure.ac:15: installing './compile'
configure.ac:13: installing './config.guess'
configure.ac:13: installing './config.sub'
configure.ac:3: installing './install-sh'
configure.ac:3: installing './missing'
cluster/Makefile.am: installing './depcomp'
make[1]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds'
   dh_auto_configure -i
   debian/rules override_dh_auto_build-indep
make[1]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds'
dh_auto_build -- docs
	make -j4 "INSTALL=install --strip-program=true" docs
make[2]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds'
doxygen
warning: Tag 'TCL_SUBST' at line 237 of file 'Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'COLS_IN_ALPHA_INDEX' at line 1001 of file 'Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'PERL_PATH' at line 2054 of file 'Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'MSCGEN_PATH' at line 2076 of file 'Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: tag INPUT: input source 'deps/libbdsg/src' does not exist
warning: tag INPUT: input source 'deps/libbdsg/include/bdsg' does not exist
warning: source 'deps/libbdsg/src' is not a readable file or directory... skipping.
warning: source 'deps/libbdsg/include/bdsg' is not a readable file or directory... skipping.
Adding custom extension mapping: 'proto' will be treated as language 'c++'
Doxygen version used: 1.9.1
Notice: Output directory 'doc/doxygen' does not exist. I have created it for you.
Searching for include files...
Searching for example files...
Searching for images...
Searching for dot files...
Searching for msc files...
Searching for dia files...
Searching for files to exclude
Searching INPUT for files to process...
Searching for files in directory /build/vg-t08NLS/vg-1.30.0+ds/src
Searching for files in directory /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms
Searching for files in directory /build/vg-t08NLS/vg-1.30.0+ds/src/io
Searching for files in directory /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand
Searching for files in directory /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src
Searching for files in directory /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph
Searching for files in directory /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src
Searching for files in directory /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io
Searching for files in directory /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/deps
Reading and parsing tag files
Parsing files
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/aligner.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/aligner.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/aligner.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/alignment.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/alignment.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/alignment.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/alignment.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/annotation.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/annotation.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/augment.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/augment.hpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/banded_global_aligner.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/banded_global_aligner.hpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/build_index.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/build_index.hpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/cactus.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/cactus.hpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/cactus_snarl_finder.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/cactus_snarl_finder.hpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/cluster.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/cluster.hpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/constructor.hpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/convert.hpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/crash.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/dagified_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/dagified_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/deconstructor.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/deconstructor.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/deletion_aligner.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/deletion_aligner.hpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/dozeu_interface.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/dozeu_pinning_overlay.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/endianness.hpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/entropy.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/flow_sort.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/flow_sort.hpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/funnel.cpp...
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Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/funnel.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/funnel.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/gapless_extender.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/gapless_extender.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/gapless_extender.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/gapless_extender.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/gbwt_helper.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/gbwt_helper.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/gbwt_helper.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/gbwt_helper.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/genome_state.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/genome_state.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/genome_state.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/genome_state.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/genotyper.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/genotyper.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/genotyper.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/genotyper.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/gfa.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/gfa.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/gfa.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/gfa.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/gff_reader.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/gff_reader.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/gff_reader.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/gff_reader.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/graph_caller.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/graph_caller.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/graph_caller.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/graph_caller.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/graph_synchronizer.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/graph_synchronizer.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/graph_synchronizer.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/graph_synchronizer.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/handle.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/handle.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_extracter.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_extracter.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_extracter.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_extracter.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_indexer.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_indexer.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_indexer.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_indexer.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/haplotypes.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/haplotypes.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/haplotypes.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/haplotypes.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/hash_map.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/hash_map.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/homogenizer.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/homogenizer.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/homogenizer.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/homogenizer.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/hts_alignment_emitter.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/hts_alignment_emitter.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/hts_alignment_emitter.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/hts_alignment_emitter.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/identity_overlay.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/identity_overlay.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/identity_overlay.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/identity_overlay.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/incremental_subgraph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/incremental_subgraph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/incremental_subgraph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/incremental_subgraph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/index_manager.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/index_manager.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/index_manager.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/index_manager.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/index_registry.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/index_registry.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/index_registry.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/index_registry.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/indexed_vg.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/indexed_vg.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/indexed_vg.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/indexed_vg.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/integrated_snarl_finder.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/integrated_snarl_finder.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/integrated_snarl_finder.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/integrated_snarl_finder.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/mapper.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/mapper.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/mapper.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/mapper.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/mcmc_caller.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/mcmc_caller.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/mcmc_caller.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/mcmc_caller.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/mcmc_genotyper.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/mcmc_genotyper.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/mcmc_genotyper.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/mcmc_genotyper.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/mem.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/mem.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/mem.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/mem.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/memoizing_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/memoizing_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/memoizing_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/memoizing_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/memusage.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/memusage.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/memusage.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/memusage.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/min_distance.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/min_distance.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/min_distance.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/min_distance.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/minimizer_mapper.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/minimizer_mapper.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/minimizer_mapper.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/minimizer_mapper.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/msa_converter.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/msa_converter.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/msa_converter.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/msa_converter.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment_emitter.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment_emitter.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment_emitter.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment_emitter.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_mapper.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_mapper.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_mapper.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_mapper.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/name_mapper.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/name_mapper.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/name_mapper.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/name_mapper.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/nested_traversal_finder.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/nested_traversal_finder.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/nested_traversal_finder.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/nested_traversal_finder.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/nodeside.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/nodeside.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/nodetraversal.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/nodetraversal.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/null_masking_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/null_masking_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/null_masking_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/null_masking_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/option.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/option.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/option.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/option.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/packer.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/packer.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/packer.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/packer.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/path.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/path.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/path.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/path.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/path_component_index.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/path_component_index.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/path_component_index.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/path_component_index.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/path_index.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/path_index.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/path_index.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/path_index.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/path_subgraph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/path_subgraph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/path_subgraph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/path_subgraph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/phased_genome.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/phased_genome.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/phased_genome.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/phased_genome.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/pictographs.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/pictographs.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/position.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/position.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/position.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/position.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/preflight.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/preflight.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/preflight.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/preflight.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/progressive.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/progressive.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/progressive.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/progressive.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/qual_adj_xdrop_aligner.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/qual_adj_xdrop_aligner.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/rare_variant_simplifier.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/rare_variant_simplifier.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/rare_variant_simplifier.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/rare_variant_simplifier.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/region.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/region.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/region.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/region.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/region_expander.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/region_expander.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/region_expander.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/region_expander.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/reverse_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/reverse_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/reverse_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/reverse_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/sampler.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/sampler.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/sampler.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/sampler.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/scanner.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/scanner.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/scanner.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/scanner.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/seed_clusterer.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/seed_clusterer.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/seed_clusterer.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/seed_clusterer.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/sequence_complexity.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/sequence_complexity.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/small_bitset.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/small_bitset.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/small_snarl_simplifier.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/small_snarl_simplifier.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/small_snarl_simplifier.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/small_snarl_simplifier.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/snarl_caller.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/snarl_caller.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/snarl_caller.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/snarl_caller.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/source_sink_overlay.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/source_sink_overlay.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/source_sink_overlay.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/source_sink_overlay.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/splicing.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/splicing.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/splicing.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/splicing.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/split_strand_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/split_strand_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/split_strand_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/split_strand_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/srpe.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/srpe.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/srpe.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/srpe.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/ssw_aligner.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/ssw_aligner.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/ssw_aligner.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/ssw_aligner.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/statistics.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/statistics.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/statistics.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/statistics.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/stream_sorter.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_sorter.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/stream_sorter.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_sorter.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subgraph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subgraph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subgraph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subgraph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subgraph_overlay.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subgraph_overlay.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subgraph_overlay.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subgraph_overlay.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/surjecting_alignment_emitter.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/surjecting_alignment_emitter.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/surjecting_alignment_emitter.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/surjecting_alignment_emitter.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/surjector.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/surjector.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/surjector.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/surjector.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/swap_remove.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/swap_remove.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/transcriptome.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/transcriptome.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/transcriptome.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/transcriptome.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/translator.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/translator.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/translator.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/translator.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/traversal_finder.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/traversal_finder.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/traversal_finder.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/traversal_finder.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/traversal_support.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/traversal_support.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/traversal_support.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/traversal_support.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/tree_subgraph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/tree_subgraph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/tree_subgraph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/tree_subgraph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/types.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/types.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/utility.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/utility.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/utility.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/utility.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/variant_adder.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/variant_adder.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/variant_adder.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/variant_adder.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/variant_recall.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/variant_recall.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/variant_recall.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/variant_recall.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/vcf_buffer.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/vcf_buffer.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/vcf_buffer.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/vcf_buffer.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/vectorizer.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/vectorizer.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/vectorizer.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/vectorizer.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/version.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/version.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/version.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/version.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/vg.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/vg.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/vg.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/vg.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/vg_set.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/vg_set.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/vg_set.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/vg_set.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/viz.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/viz.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/viz.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/viz.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/wang_hash.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/wang_hash.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/watchdog.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/watchdog.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/watchdog.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/watchdog.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/xdrop_aligner.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/xdrop_aligner.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/a_star.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/a_star.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/alignment_path_offsets.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/alignment_path_offsets.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/alignment_path_offsets.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/alignment_path_offsets.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/approx_path_distance.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/approx_path_distance.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/approx_path_distance.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/approx_path_distance.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/coverage_depth.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/coverage_depth.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/coverage_depth.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/coverage_depth.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/dfs.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/dfs.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/dfs.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/dfs.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/disjoint_components.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/disjoint_components.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/disjoint_components.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/disjoint_components.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/distance_to_head.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/distance_to_head.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/distance_to_head.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/distance_to_head.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/distance_to_tail.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/distance_to_tail.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/distance_to_tail.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/distance_to_tail.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/expand_context.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/expand_context.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/expand_context.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/expand_context.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_connecting_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_connecting_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_connecting_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_connecting_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_containing_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_containing_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_containing_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_containing_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_extending_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_extending_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_extending_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_extending_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/gfa_to_handle.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/gfa_to_handle.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/gfa_to_handle.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/gfa_to_handle.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/id_sort.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/id_sort.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/id_sort.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/id_sort.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/jump_along_path.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/jump_along_path.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/jump_along_path.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/jump_along_path.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/k_widest_paths.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/k_widest_paths.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/k_widest_paths.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/k_widest_paths.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/merge.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/merge.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/merge.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/merge.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/nearest_offsets_in_paths.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/nearest_offsets_in_paths.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/nearest_offsets_in_paths.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/nearest_offsets_in_paths.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/next_pos_chars.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/next_pos_chars.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/next_pos_chars.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/next_pos_chars.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/normalize.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/normalize.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/normalize.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/normalize.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/path_string.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/path_string.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/path_string.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/path_string.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/prune.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/prune.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/prune.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/prune.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/ref_path_distance.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/ref_path_distance.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/ref_path_distance.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/ref_path_distance.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/shortest_cycle.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/shortest_cycle.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/shortest_cycle.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/shortest_cycle.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/simplify_siblings.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/simplify_siblings.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/simplify_siblings.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/simplify_siblings.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/sorted_id_ranges.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/sorted_id_ranges.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/sorted_id_ranges.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/sorted_id_ranges.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/subgraph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/subgraph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/subgraph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/subgraph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/three_edge_connected_components.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/three_edge_connected_components.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/three_edge_connected_components.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/three_edge_connected_components.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/to_gfa.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/to_gfa.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/to_gfa.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/to_gfa.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/converted_hash_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/converted_hash_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/json_stream_helper.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/json_stream_helper.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/load_proto_to_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/load_proto_to_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/load_proto_to_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/load_proto_to_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_libvg_io.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_libvg_io.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_libvg_io.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_libvg_io.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_distance_index.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_distance_index.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_distance_index.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_distance_index.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gbwt.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gbwt.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gbwt.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gbwt.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gbwtgraph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gbwtgraph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gbwtgraph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gbwtgraph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gcsa.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gcsa.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gcsa.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_gcsa.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_hash_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_hash_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_hash_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_hash_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_lcp.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_lcp.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_lcp.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_lcp.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_minimizer.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_minimizer.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_minimizer.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_minimizer.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_odgi.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_odgi.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_odgi.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_odgi.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_packed_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_packed_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_packed_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_packed_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_r_index.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_r_index.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_r_index.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_r_index.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_snarl_manager.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_snarl_manager.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_snarl_manager.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_snarl_manager.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_vg.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_vg.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_vg.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_vg.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_xg.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_xg.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_xg.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/register_loader_saver_xg.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/io/save_handle_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/io/save_handle_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/add_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/add_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/align_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/align_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/annotate_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/annotate_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/augment_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/augment_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/autoindex_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/autoindex_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/benchmark_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/benchmark_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/call_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/call_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/chunk_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/chunk_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/circularize_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/circularize_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/cluster_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/cluster_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/combine_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/combine_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/concat_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/concat_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/construct_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/construct_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/convert_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/convert_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/deconstruct_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/deconstruct_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/depth_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/depth_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/dotplot_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/dotplot_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/explode_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/explode_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/filter_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/filter_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/find_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/find_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/gamcompare_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/gamcompare_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/gampcompare_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/gampcompare_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/gamsort_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/gamsort_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/gbwt_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/gbwt_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/genotype_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/genotype_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/giraffe_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/giraffe_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/help_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/help_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/ids_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/ids_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/index_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/index_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/inject_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/inject_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/join_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/join_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/kmers_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/kmers_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/map_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/map_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/mcmc_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/mcmc_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/minimizer_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/minimizer_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/mod_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/mod_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/mpmap_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/mpmap_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/msga_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/msga_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/pack_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/pack_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/paths_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/paths_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/prune_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/prune_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/recalibrate_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/recalibrate_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/rna_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/rna_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/sift_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/sift_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/sim_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/sim_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/simplify_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/simplify_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/snarls_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/snarls_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/sort_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/sort_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/srpe_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/srpe_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/stats_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/stats_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/surject_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/surject_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/test_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/test_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/trace_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/trace_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/translate_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/translate_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/validate_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/validate_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/vectorize_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/vectorize_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/version_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/version_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/view_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/view_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/viz_main.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/viz_main.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/unittest/driver.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/unittest/driver.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/src/unittest/driver.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/src/unittest/driver.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/buildable_snarl_decomposition.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/buildable_snarl_decomposition.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/snarl_decomposition.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/snarl_decomposition.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/util.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/util.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/bin2ascii.h...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/bin2ascii.h...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/edit.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/edit.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/registry.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/registry.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/stream.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/stream.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_io.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_io.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/blocked_gzip_input_stream.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/blocked_gzip_input_stream.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/blocked_gzip_output_stream.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/blocked_gzip_output_stream.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/edit.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/edit.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/fdstream.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/fdstream.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/hfile_cppstream.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/hfile_cppstream.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/hfile_internal.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/hfile_internal.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/json2pb.h...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/json2pb.h...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/loader.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/loader.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_emitter.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_emitter.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_emitter.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_emitter.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/build/vg-t08NLS/vg-1.30.0+ds/src/qual_adj_xdrop_aligner.cpp:2: warning: the name 'qual_adj_xdrop_aliigner.cpp' supplied as the argument in the \file statement is not an input file
/build/vg-t08NLS/vg-1.30.0+ds/src/xdrop_aligner.cpp:2: warning: the name 'xdrop_aliigner.cpp' supplied as the argument in the \file statement is not an input file
/build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_containing_graph.hpp:5: warning: the name 'extract_containing_graphs.hpp' supplied as the argument in the \file statement is not an input file
/build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/extract_extending_graph.hpp:5: warning: the name 'extract_extending_graphs.hpp' supplied as the argument in the \file statement is not an input file
/build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp:5: warning: the name 'handle_graphs.cpp' supplied as the argument in the \file statement is not an input file
/build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp:5: warning: the name 'stream_multiplexer.chpp' supplied as the argument in the \file statement is not an input file
/build/vg-t08NLS/vg-1.30.0+ds/src/alignment.hpp:281: warning: no matching file member found for 
void vg::parse_bed_regions(istream &bedstream, const handlegraph::PathPositionHandleGraph *graph, vector< vg::Alignment > *out_alignments)
Possible candidates:
 'void parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)' at line 1773 of file /build/vg-t08NLS/vg-1.30.0+ds/src/alignment.cpp
 'void parse_bed_regions(const string &bed_path, vector< Region > &out_regions, vector< string > *out_names)' at line 28 of file /build/vg-t08NLS/vg-1.30.0+ds/src/region.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/alignment.hpp:282: warning: no matching file member found for 
void vg::parse_gff_regions(istream &gtfstream, const handlegraph::PathPositionHandleGraph *graph, vector< vg::Alignment > *out_alignments)
Possible candidates:
 'void parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)' at line 1856 of file /build/vg-t08NLS/vg-1.30.0+ds/src/alignment.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/benchmark.hpp:48: warning: no matching file member found for 
ostream & vg::operator<<(ostream &out, const vg::BenchmarkResult &result)
Possible candidates:
 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/vg-t08NLS/vg-1.30.0+ds/src/benchmark.cpp
 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.cpp
 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.cpp
 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/vg-t08NLS/vg-1.30.0+ds/src/mem.cpp
 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodeside.hpp
 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodetraversal.hpp
 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/path.cpp
 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.cpp
 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.cpp
 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/vg-t08NLS/vg-1.30.0+ds/src/types.hpp
 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.cpp
 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.cpp
 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp

/build/vg-t08NLS/vg-1.30.0+ds/src/cluster.hpp:769: warning: no matching file member found for 
bdsg::HashGraph vg::cluster_subgraph_containing(const handlegraph::HandleGraph &base, const vg::Alignment &aln, const vector< vg::vg::MaximalExactMatch > &cluster, const vg::GSSWAligner *aligner)
Possible candidates:
 'bdsg::HashGraph cluster_subgraph_containing(const HandleGraph &base, const Alignment &aln, const vector< vg::MaximalExactMatch > &cluster, const GSSWAligner *aligner)' at line 3827 of file /build/vg-t08NLS/vg-1.30.0+ds/src/cluster.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/cluster.hpp:772: warning: no matching file member found for 
bdsg::HashGraph vg::cluster_subgraph_walk(const handlegraph::HandleGraph &base, const vg::Alignment &aln, const vector< vg::vg::MaximalExactMatch > &mems, double expansion)
Possible candidates:
 'bdsg::HashGraph cluster_subgraph_walk(const HandleGraph &base, const Alignment &aln, const vector< vg::MaximalExactMatch > &mems, double expansion)' at line 3848 of file /build/vg-t08NLS/vg-1.30.0+ds/src/cluster.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.hpp:504: warning: no matching file member found for 
ostream & vg::operator<<(ostream &stream, const vg::Support &support)
Possible candidates:
 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/vg-t08NLS/vg-1.30.0+ds/src/benchmark.cpp
 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.cpp
 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.cpp
 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/vg-t08NLS/vg-1.30.0+ds/src/mem.cpp
 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodeside.hpp
 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodetraversal.hpp
 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/path.cpp
 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.cpp
 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.cpp
 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/vg-t08NLS/vg-1.30.0+ds/src/types.hpp
 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.cpp
 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.cpp
 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp

/build/vg-t08NLS/vg-1.30.0+ds/src/gfa.hpp:21: warning: no matching file member found for 
void vg::graph_to_gfa(const unique_ptr< handlegraph::PathHandleGraph > &graph, ostream &out)
Possible candidates:
 'void graph_to_gfa(const unique_ptr< PathHandleGraph > &graph, ostream &out)' at line 9 of file /build/vg-t08NLS/vg-1.30.0+ds/src/gfa.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_extracter.hpp:47: warning: no matching file member found for 
void vg::output_graph_with_embedded_paths(ostream &subgraph_ostream, vector< pair< vector< gbwt::node_type >, int >> &haplotype_list, const handlegraph::HandleGraph &source, bool json=true)
Possible candidates:
 'Graph output_graph_with_embedded_paths(vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source)' at line 71 of file /build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_extracter.cpp
 'void output_graph_with_embedded_paths(ostream &subgraph_ostream, vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source, bool json)' at line 88 of file /build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_extracter.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_extracter.hpp:54: warning: no matching file member found for 
void vg::output_haplotype_counts(ostream &annotation_ostream, vector< pair< vector< gbwt::node_type >, int >> &haplotype_list)
Possible candidates:
 'void output_haplotype_counts(ostream &annotation_ostream, vector< pair< thread_t, int >> &haplotype_list)' at line 64 of file /build/vg-t08NLS/vg-1.30.0+ds/src/haplotype_extracter.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/kmer.hpp:49: warning: no matching file member found for 
ostream & vg::operator<<(ostream &out, const vg::kmer_t &kmer)
Possible candidates:
 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/vg-t08NLS/vg-1.30.0+ds/src/benchmark.cpp
 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.cpp
 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.cpp
 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/vg-t08NLS/vg-1.30.0+ds/src/mem.cpp
 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodeside.hpp
 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodetraversal.hpp
 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/path.cpp
 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.cpp
 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.cpp
 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/vg-t08NLS/vg-1.30.0+ds/src/types.hpp
 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.cpp
 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.cpp
 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp

/build/vg-t08NLS/vg-1.30.0+ds/src/kmer.hpp:62: warning: no matching file member found for 
void vg::write_gcsa_kmers(const handlegraph::HandleGraph &graph, int kmer_size, ostream &out, size_t &size_limit, long long int head_id, long long int tail_id)
Possible candidates:
 'void write_gcsa_kmers(const HandleGraph &graph, int kmer_size, ostream &out, size_t &size_limit, id_t head_id, id_t tail_id)' at line 227 of file /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment.hpp:379: warning: no matching file member found for 
void vg::view_multipath_alignment(ostream &out, const vg::multipath_alignment_t &multipath_aln, const handlegraph::HandleGraph &handle_graph)
Possible candidates:
 'void view_multipath_alignment(ostream &out, const multipath_alignment_t &multipath_aln, const HandleGraph &handle_graph)' at line 3889 of file /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment.hpp:382: warning: no matching file member found for 
void vg::view_multipath_alignment_as_dot(ostream &out, const vg::multipath_alignment_t &multipath_aln, bool show_graph=false)
Possible candidates:
 'void view_multipath_alignment_as_dot(ostream &out, const multipath_alignment_t &multipath_aln, bool show_graph)' at line 3994 of file /build/vg-t08NLS/vg-1.30.0+ds/src/multipath_alignment.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/path.hpp:40: warning: no matching file member found for 
ostream & vg::operator<<(ostream &out, vg::mapping_t mapping)
Possible candidates:
 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/vg-t08NLS/vg-1.30.0+ds/src/benchmark.cpp
 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.cpp
 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.cpp
 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/vg-t08NLS/vg-1.30.0+ds/src/mem.cpp
 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodeside.hpp
 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodetraversal.hpp
 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/path.cpp
 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.cpp
 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.cpp
 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/vg-t08NLS/vg-1.30.0+ds/src/types.hpp
 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.cpp
 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.cpp
 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp

/build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.hpp:292: warning: no matching file member found for 
ostream & vg::operator<<(ostream &os, const vg::Counts &counts)
Possible candidates:
 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/vg-t08NLS/vg-1.30.0+ds/src/benchmark.cpp
 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.cpp
 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.cpp
 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/vg-t08NLS/vg-1.30.0+ds/src/mem.cpp
 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodeside.hpp
 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodetraversal.hpp
 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/path.cpp
 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.cpp
 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.cpp
 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/vg-t08NLS/vg-1.30.0+ds/src/types.hpp
 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.cpp
 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.cpp
 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp

/build/vg-t08NLS/vg-1.30.0+ds/src/snarls.hpp:806: warning: no matching file member found for 
ostream & vg::operator<<(ostream &out, const vg::Visit &visit)
Possible candidates:
 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/vg-t08NLS/vg-1.30.0+ds/src/benchmark.cpp
 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.cpp
 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.cpp
 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/vg-t08NLS/vg-1.30.0+ds/src/mem.cpp
 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodeside.hpp
 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodetraversal.hpp
 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/path.cpp
 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.cpp
 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.cpp
 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/vg-t08NLS/vg-1.30.0+ds/src/types.hpp
 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.cpp
 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.cpp
 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp

/build/vg-t08NLS/vg-1.30.0+ds/src/snarls.hpp:846: warning: no matching file member found for 
ostream & vg::operator<<(ostream &out, const vg::Snarl &snarl)
Possible candidates:
 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/vg-t08NLS/vg-1.30.0+ds/src/benchmark.cpp
 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.cpp
 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.cpp
 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/vg-t08NLS/vg-1.30.0+ds/src/mem.cpp
 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodeside.hpp
 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodetraversal.hpp
 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/path.cpp
 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.cpp
 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.cpp
 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/vg-t08NLS/vg-1.30.0+ds/src/types.hpp
 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.cpp
 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.cpp
 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp

/build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.hpp:99: warning: no matching file member found for 
ostream & vg::operator<<(ostream &out, const vg::BitString &bs)
Possible candidates:
 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/vg-t08NLS/vg-1.30.0+ds/src/benchmark.cpp
 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/vg-t08NLS/vg-1.30.0+ds/src/genotypekit.cpp
 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/vg-t08NLS/vg-1.30.0+ds/src/kmer.cpp
 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/vg-t08NLS/vg-1.30.0+ds/src/mem.cpp
 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodeside.hpp
 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/vg-t08NLS/vg-1.30.0+ds/src/nodetraversal.hpp
 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/path.cpp
 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/vg-t08NLS/vg-1.30.0+ds/src/phase_unfolder.cpp
 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/vg-t08NLS/vg-1.30.0+ds/src/readfilter.cpp
 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/vg-t08NLS/vg-1.30.0+ds/src/snarls.cpp
 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/vg-t08NLS/vg-1.30.0+ds/src/stream_index.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/vg-t08NLS/vg-1.30.0+ds/src/types.hpp
 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/kmer.cpp
 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/walk.cpp
 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/subcommand.cpp
 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/xg.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp
 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp

/build/vg-t08NLS/vg-1.30.0+ds/src/utility.hpp:69: warning: no matching file member found for 
void vg::write_fasta_sequence(const std::string &name, const std::string &sequence, ostream &os, size_t width=80)
Possible candidates:
 'void write_fasta_sequence(const std::string &name, const std::string &sequence, ostream &os, size_t width)' at line 273 of file /build/vg-t08NLS/vg-1.30.0+ds/src/utility.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/utility.hpp:423: warning: no matching file member found for 
void vg::get_input_file(int &optind, int argc, char **argv, function< void(istream &)> callback)
Possible candidates:
 'void get_input_file(int &optind, int argc, char **argv, function< void(istream &)> callback)' at line 446 of file /build/vg-t08NLS/vg-1.30.0+ds/src/utility.cpp
 'void get_input_file(const string &file_name, function< void(istream &)> callback)' at line 491 of file /build/vg-t08NLS/vg-1.30.0+ds/src/utility.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/utility.hpp:436: warning: no matching file member found for 
void vg::get_input_file(const string &file_name, function< void(istream &)> callback)
Possible candidates:
 'void get_input_file(int &optind, int argc, char **argv, function< void(istream &)> callback)' at line 446 of file /build/vg-t08NLS/vg-1.30.0+ds/src/utility.cpp
 'void get_input_file(const string &file_name, function< void(istream &)> callback)' at line 491 of file /build/vg-t08NLS/vg-1.30.0+ds/src/utility.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/coverage_depth.hpp:22: warning: no matching file member found for 
void vg::algorithms::packed_depths(const vg::Packer &packer, const string &path_name, size_t min_coverage, ostream &out_stream)
Possible candidates:
 'void packed_depths(const Packer &packer, const string &path_name, size_t min_coverage, ostream &out_stream)' at line 10 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/coverage_depth.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/gfa_to_handle.hpp:50: warning: no matching file member found for 
void vg::algorithms::gfa_to_path_handle_graph_in_memory(istream &in, handlegraph::MutablePathMutableHandleGraph *graph)
Possible candidates:
 'void gfa_to_path_handle_graph_in_memory(istream &in, MutablePathMutableHandleGraph *graph)' at line 246 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/gfa_to_handle.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/to_gfa.hpp:13: warning: no matching file member found for 
void vg::algorithms::to_gfa(const handlegraph::PathHandleGraph &graph, ostream &out)
Possible candidates:
 'void to_gfa(const PathHandleGraph &graph, ostream &out)' at line 8 of file /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/to_gfa.cpp

/build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/chunk_main.cpp:853: warning: no matching file member found for 
int split_gam(istream &gam_stream, size_t chunk_size, const string &out_prefix, size_t gam_buffer_size)
Possible candidates:
 'static int split_gam(istream &gam_stream, size_t chunk_size, const string &out_prefix, size_t gam_buffer_size=100)' at line 853 of file /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/chunk_main.cpp

/build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:64: warning: no matching file member found for 
load_function_t vg::io::wrap_bare_loader(function< void *(istream &)> istream_loader)
Possible candidates:
 'auto wrap_bare_loader(function< void *(istream &)> istream_loader) -> load_function_t' at line 105 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/registry.cpp

/build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:70: warning: no matching file member found for 
void vg::io::with_function_calling_stream(const function< void(const string &)> &emit_message, const function< void(ostream &)> &use_stream)
Possible candidates:
 'void with_function_calling_stream(const message_consumer_function_t &emit_message, const function< void(ostream &)> &use_stream)' at line 197 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/registry.cpp

/build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:76: warning: no matching file member found for 
save_function_t vg::io::wrap_bare_saver(const function< void(void *, ostream &)> ostream_saver)
Possible candidates:
 'auto wrap_bare_saver(function< void(const void *, ostream &)> ostream_saver) -> save_function_t' at line 312 of file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/registry.cpp

/deps/libvgio/include/vg/io/stream.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/vpkg.hpp...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/vpkg.hpp...
Preprocessing /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/deps/vg.proto...
Parsing file /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/deps/vg.proto...
Building macro definition list...
Building group list...
Building directory list...
Building namespace list...
Building file list...
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Computing nesting relations for classes...
Associating documentation with classes...
Building example list...
Searching for enumerations...
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Searching for members imported via using declarations...
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Building interface member list...
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Searching for documented defines...
Computing class inheritance relations...
Computing class usage relations...
Flushing cached template relations that have become invalid...
Computing class relations...
Add enum values to enums...
Searching for member function documentation...
Creating members for template instances...
Building page list...
Search for main page...
Computing page relations...
Determining the scope of groups...
Sorting lists...
Determining which enums are documented
Computing member relations...
Building full member lists recursively...
Adding members to member groups.
Computing member references...
Inheriting documentation...
Generating disk names...
Adding source references...
Adding xrefitems...
Sorting member lists...
Setting anonymous enum type...
Computing dependencies between directories...
Generating citations page...
Counting members...
Counting data structures...
Resolving user defined references...
Finding anchors and sections in the documentation...
Transferring function references...
Combining using relations...
Adding members to index pages...
Correcting members for VHDL...
Computing tooltip texts...
Generating style sheet...
Generating search indices...
Generating example documentation...
Generating file sources...
Generating file documentation...
Generating docs for file deps/libhandlegraph/src/append_graph.cpp...
Generating docs for file deps/libhandlegraph/src/apply_orientations.cpp...
Generating docs for file deps/libhandlegraph/src/are_equivalent.cpp...
Generating docs for file deps/libhandlegraph/src/copy_graph.cpp...
Generating docs for file deps/libhandlegraph/src/count_walks.cpp...
Generating docs for file deps/libhandlegraph/src/dagify.cpp...
Generating docs for file deps/libhandlegraph/src/deletable_handle_graph.cpp...
Generating docs for file deps/libhandlegraph/src/dijkstra.cpp...
Generating docs for file deps/libhandlegraph/src/eades_algorithm.cpp...
Generating docs for file deps/libhandlegraph/src/extend.cpp...
Generating docs for file deps/libhandlegraph/src/find_shortest_paths.cpp...
Generating docs for file deps/libhandlegraph/src/find_tips.cpp...
Generating docs for file deps/libhandlegraph/src/handle_graph.cpp...
Generating docs for file deps/libhandlegraph/src/include/handlegraph/buildable_snarl_decomposition.hpp...
Generating docs for file deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp...
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Generating docs for file deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp...
Generating docs for file deps/libhandlegraph/src/include/handlegraph/iteratee.hpp...
Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp...
Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp...
Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp...
Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp...
Generating docs for file deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp...
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Generating docs for file deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp...
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Generating docs for file deps/libvgio/src/blocked_gzip_output_stream.cpp...
Generating docs for file deps/libvgio/src/edit.cpp...
Generating docs for file deps/libvgio/src/hfile_cppstream.cpp...
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Generating docs for compound vg::SplicedHTSAlignmentEmitter...
Generating docs for compound vg::IdentityOverlay...
Generating docs for compound vg::IncrementalSubgraph...
Generating docs for compound vg::IndexManager...
Generating docs for compound vg::IndexingParameters...
Generating docs for compound vg::VGIndexes...
Generating docs for compound vg::IndexRegistry...
Generating docs for compound vg::IndexFile...
Generating docs for compound vg::IndexRecipe...
Generating docs for compound vg::InsufficientInputException...
Generating docs for compound vg::IndexedVG...
Generating docs for nested compound vg::IndexedVG::CacheEntry...
Generating docs for compound vg::IntegratedSnarlFinder...
Generating docs for nested compound vg::IntegratedSnarlFinder::MergedAdjacencyGraph...
Generating docs for compound vg::kmer_t...
Generating docs for compound vg::AlignmentChainModelVertex...
Generating docs for compound vg::AlignmentChainModel...
Generating docs for compound vg::FragmentLengthDistribution...
Generating docs for compound vg::PairedEndMapper...
Generating docs for compound vg::BaseMapper...
Generating docs for compound vg::FragmentLengthStatistics...
Generating docs for compound vg::Mapper...
Generating docs for compound vg::MCMCCaller...
Generating docs for compound vg::MCMCGenotyper...
Generating docs for compound vg::MaximalExactMatch...
Generating docs for compound vg::MemoizingGraph...
Generating docs for compound vg::MinimumDistanceIndex...
Generating docs for nested compound vg::MinimumDistanceIndex::ChainIndex...
Generating docs for nested compound vg::MinimumDistanceIndex::SnarlIndex...
Generating docs for compound vg::MIPayload...
Generating docs for compound vg::MinimizerMapper...
Generating docs for nested compound vg::MinimizerMapper::Minimizer...
Generating docs for compound vg::MSAConverter...
Generating docs for compound vg::MultipathProblem...
Generating docs for compound vg::connection_t...
Generating docs for compound vg::subpath_t...
Generating docs for compound vg::multipath_alignment_t...
Generating docs for compound vg::MultipathAlignmentEmitter...
Generating docs for compound vg::PathNode...
Generating docs for compound vg::MultipathAlignmentGraph...
Generating docs for compound vg::MultipathMapper...
Generating docs for compound vg::NameMapper...
Generating docs for compound vg::NestedTraversalFinder...
Generating docs for compound vg::NodeSide...
Generating docs for compound vg::wang_hash< NodeSide >...
Generating docs for compound vg::NodeTraversal...
Generating docs for compound vg::wang_hash< NodeTraversal >...
Generating docs for compound vg::NullMaskingGraph...
Generating docs for compound vg::OptionInterface...
Generating docs for compound vg::Configurable...
Generating docs for compound vg::ConfigurableParser...
Generating docs for compound vg::OptionValueParser...
Generating docs for compound vg::OptionValueParser< vector< Item > >...
Generating docs for compound vg::BaseOption...
Generating docs for compound vg::Option...
Generating docs for compound vg::Option< vector< Item >, Parser >...
Generating docs for compound vg::Packer...
Generating docs for compound vg::Packers...
Generating docs for compound vg::mapping_t...
Generating docs for compound vg::Paths...
Generating docs for compound vg::edit_t...
Generating docs for compound vg::path_mapping_t...
Generating docs for compound vg::path_t...
Generating docs for compound vg::PathComponentIndex...
Generating docs for compound vg::PathIndex...
Generating docs for compound vg::PathSubgraph...
Generating docs for compound vg::PathBranch...
Generating docs for compound vg::PhaseUnfolder...
Generating docs for compound vg::PhasedGenome...
Generating docs for nested compound vg::PhasedGenome::Haplotype...
Generating docs for nested compound vg::PhasedGenome::HaplotypeNode...
Generating docs for nested compound vg::PhasedGenome::iterator...
Generating docs for compound vg::Pictographs...
Generating docs for compound vg::position_t...
Generating docs for compound vg::Progressive...
Generating docs for compound vg::RareVariantSimplifier...
Generating docs for compound vg::ReadFilter...
Generating docs for compound vg::Counts...
Generating docs for compound vg::Region...
Generating docs for compound vg::RegionExpander...
Generating docs for compound vg::ReverseGraph...
Generating docs for compound vg::Sampler...
Generating docs for compound vg::NGSSimulator...
Generating docs for nested compound vg::NGSSimulator::MarkovDistribution...
Generating docs for compound vg::PositionIDScanner...
Generating docs for compound vg::IDScanner...
Generating docs for compound vg::WrappingPositionScanner...
Generating docs for compound vg::SnarlSeedClusterer...
Generating docs for nested compound vg::SnarlSeedClusterer::Cluster...
Generating docs for nested compound vg::SnarlSeedClusterer::NetgraphNode...
Generating docs for nested compound vg::SnarlSeedClusterer::NodeClusters...
Generating docs for nested compound vg::SnarlSeedClusterer::Seed...
Generating docs for nested compound vg::SnarlSeedClusterer::TreeState...
Generating docs for compound vg::SeqComplexity...
Generating docs for compound vg::SmallBitset...
Generating docs for compound vg::SmallSnarlSimplifier...
Generating docs for compound vg::SnarlCaller...
Generating docs for nested compound vg::SnarlCaller::CallInfo...
Generating docs for compound vg::SupportBasedSnarlCaller...
Generating docs for compound vg::RatioSupportSnarlCaller...
Generating docs for compound vg::PoissonSupportSnarlCaller...
Generating docs for nested compound vg::PoissonSupportSnarlCaller::PoissonCallInfo...
Generating docs for compound vg::SnarlFinder...
Generating docs for compound vg::HandleGraphSnarlFinder...
Generating docs for compound vg::ChainIterator...
Generating docs for compound vg::NetGraph...
Generating docs for compound vg::SnarlManager...
Generating docs for nested compound vg::SnarlManager::SnarlRecord...
Generating docs for compound vg::SourceSinkOverlay...
Generating docs for compound vg::SpliceMotifs...
Generating docs for compound vg::SpliceRegion...
Generating docs for compound vg::JoinedSpliceGraph...
Generating docs for compound vg::StrandSplitGraph...
Generating docs for compound vg::BREAKPOINT...
Generating docs for compound vg::DepthMap...
Generating docs for compound vg::SRPE...
Generating docs for compound vg::SSWAligner...
Generating docs for compound vg::uniform_real_distribution...
Generating docs for compound vg::normal_distribution...
Generating docs for compound vg::WideningPRNG...
Generating docs for compound vg::uniform_int_distribution...
Generating docs for compound vg::discrete_distribution...
Generating docs for compound vg::BitString...
Generating docs for compound vg::BitStringTree...
Generating docs for nested compound vg::BitStringTree::TreeNode...
Generating docs for compound vg::StreamIndexBase...
Generating docs for compound vg::StreamIndex...
Generating docs for compound vg::StreamSorter...
Generating docs for compound vg::SubHandleGraph...
Generating docs for compound vg::SubgraphOverlay...
Generating docs for compound vg::PathSubgraphOverlay...
Generating docs for compound vg::SurjectingAlignmentEmitter...
Generating docs for compound vg::Surjector...
Generating docs for compound vg::Exon...
Generating docs for compound vg::Transcript...
Generating docs for compound vg::TranscriptPath...
Generating docs for compound vg::EditedTranscriptPath...
Generating docs for compound vg::CompletedTranscriptPath...
Generating docs for compound vg::Transcriptome...
Generating docs for compound vg::Translator...
Generating docs for compound vg::TraversalFinder...
Generating docs for compound vg::ExhaustiveTraversalFinder...
Generating docs for compound vg::SupportRestrictedTraversalFinder...
Generating docs for compound vg::ReadRestrictedTraversalFinder...
Generating docs for compound vg::PathRestrictedTraversalFinder...
Generating docs for compound vg:/build/vg-t08NLS/vg-1.30.0+ds/src/vg.hpp:894: warning: explicit link request to 'matches' could not be resolved
/build/vg-t08NLS/vg-1.30.0+ds/src/vg.hpp:894: warning: explicit link request to 'mismatches' could not be resolved
/build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/deps/vg.proto:267: warning: Unsupported xml/html tag <parentSnarlHash> found
/build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/deps/vg.proto:267: warning: Unsupported xml/html tag <parentSnarlHash> found
:PathBasedTraversalFinder...
Generating docs for compound vg::PathTraversalFinder...
Generating docs for compound vg::TrivialTraversalFinder...
Generating docs for compound vg::RepresentativeTraversalFinder...
Generating docs for compound vg::VCFTraversalFinder...
Generating docs for compound vg::FlowTraversalFinder...
Generating docs for compound vg::GBWTTraversalFinder...
Generating docs for compound vg::TraversalSupportFinder...
Generating docs for compound vg::PackedTraversalSupportFinder...
Generating docs for compound vg::CachedPackedTraversalSupportFinder...
Generating docs for compound vg::TreeSubgraph...
Generating docs for compound vg::TreeNode...
Generating docs for compound vg::Tree...
Generating docs for compound vg::IncrementIter...
Generating docs for compound vg::VariantAdder...
Generating docs for compound vg::VcfBuffer...
Generating docs for compound vg::WindowedVcfBuffer...
Generating docs for compound vg::Version...
Generating docs for compound vg::KmerPosition...
Generating docs for compound vg::VG...
Generating docs for nested compound vg::VG::Plan...
Generating docs for compound vg::VGset...
Generating docs for compound vg::Viz...
Generating docs for compound vg::Watchdog...
Generating docs for nested compound vg::Watchdog::thread_state_t...
Generating docs for compound vg::Range...
Generating docs for compound vg::is_instantiation_of...
Generating docs for compound vg::is_instantiation_of< Predicate< PredicateArgs... >, Predicate >...
Generating docs for compound vg::Graph...
Generating docs for compound vg::Node...
Generating docs for compound vg::Edge...
Generating docs for compound vg::Edit...
Generating docs for compound vg::Mapping...
Generating docs for compound vg::Position...
Generating docs for compound vg::Path...
Generating docs for compound vg::Alignment...
Generating docs for compound vg::MultipathAlignment...
Generating docs for compound vg::Subpath...
Generating docs for compound vg::Connection...
Generating docs for compound vg::KmerMatch...
Generating docs for compound vg::BasePileup...
Generating docs for compound vg::NodePileup...
Generating docs for compound vg::EdgePileup...
Generating docs for compound vg::Pileup...
Generating docs for compound vg::Snarl...
Generating docs for compound vg::Visit...
Generating docs for compound vg::SnarlTraversal...
Generating docs for compound vg::Locus...
Generating docs for compound vg::Genotype...
Generating docs for compound vg::Support...
Generating docs for compound vg::LocationSupport...
Generating docs for compound vg::Translation...
Generating docs for namespace vg::algorithms
Generating docs for compound vg::algorithms::GFAFormatError...
Generating docs for compound vg::algorithms::kmer_t...
Generating docs for compound vg::algorithms::walk_t...
Generating docs for namespace vg::io
Generating docs for compound vg::io::ConvertedHashGraph...
Generating docs for compound vg::io::JSONStreamHelper...
Generating docs for compound vg::io::hFILE_cppstream...
Generating docs for compound vg::io::AlignmentEmitter...
Generating docs for compound vg::io::NullAlignmentEmitter...
Generating docs for compound vg::io::TSVAlignmentEmitter...
Generating docs for compound vg::io::VGAlignmentEmitter...
Generating docs for compound vg::io::GafAlignmentEmitter...
Generating docs for compound vg::io::BlockedGzipInputStream...
Generating docs for compound vg::io::BlockedGzipOutputStream...
Generating docs for compound vg::io::fdoutbuf...
Generating docs for compound vg::io::fdostream...
Generating docs for compound vg::io::fdinbuf...
Generating docs for compound vg::io::fdistream...
Generating docs for compound vg::io::streaminbuf...
Generating docs for compound vg::io::streamistream...
Generating docs for compound vg::io::MessageEmitter...
Generating docs for compound vg::io::MessageIterator...
Generating docs for compound vg::io::ProtobufEmitter...
Generating docs for compound vg::io::ProtobufIterator...
Generating docs for compound vg::io::Registry...
Generating docs for nested compound vg::io::Registry::Tables...
Generating docs for compound vg::io::St/build/vg-t08NLS/vg-1.30.0+ds/src/banded_global_aligner.hpp:88: warning: Unsupported xml/html tag <IntType> found
reamMultiplexer...
Generating docs for compound vg::io::VPKG...
Generating docs for namespace vg::subcommand
Generating docs for compound vg::subcommand::Subcommand...
Generating docs for namespace vg::temp_file
Generating docs for compound vg::temp_file::Handler...
Generating docs for namespace vg::unittest
Generating docs for namespace xg
Generating docs for compound xg::XGFormatError...
Generating docs for compound xg::XG...
Generating docs for compound xg::XGPath...
Generating docs for namespace xg::temp_file
Generating docs for compound xg::temp_file::Handler...
Generating graph info page...
Generating directory documentation...
Generating index page...
Generating page index...
Generating module index...
Generating namespace index...
Generating namespace member index...
Generating annotated compound index...
Generating alphabetical compound index...
Generating hierarchical class index...
Generating member index...
Generating file index...
Generating file member index...
Generating example index...
finalizing index lists...
writing tag file...
Generating XML output...
Generating XML output for class vg::Genotyper::Affinity
Generating XML output for class vg::Aligner
Generating XML output for class vg::AlignerClient
Generating XML output for class vg::Alignment
Generating XML output for class vg::AlignmentChainModel
Generating XML output for class vg::AlignmentChainModelVertex
Generating XML output for class vg::io::AlignmentEmitter
Generating XML output for class vg::BandedGlobalAligner::AltTracebackStack
Generating XML output for class vg::Annotation
Generating XML output for class vg::AppendHaplotypeCommand
Generating XML output for class vg::AugmentedGraph
Generating XML output for class vg::BandedGlobalAligner::BABuilder
Generating XML output for class vg::BandedGlobalAligner::BAMatrix
Generating XML output for class vg::BandedGlobalAligner
Generating XML output for class vg::BaseAligner
Generating XML output for class vg::BaseMapper
Generating XML output for class vg::BaseOption
Generating XML output for class vg::BasePileup
Generating XML output for class vg::BenchmarkResult
Generating XML output for class vg::BitString
Generating XML output for class vg::BitStringTree
Generating XML output for class vg::io::BlockedGzipInputStream
Generating XML output for class vg::io::BlockedGzipOutputStream
Generating XML output for class handlegraph::BoolReturningWrapper
Generating XML output for class handlegraph::BoolReturningWrapper< Iteratee, Iterated, bool >
Generating XML output for class handlegraph::BoolReturningWrapper< Iteratee, Iterated, void >
Generating XML output for class vg::BREAKPOINT
Generating XML output for class handlegraph::BuildableSnarlDecomposition
Generating XML output for class vg::CachedPackedTraversalSupportFinder
Generating XML output for class vg::IndexedVG::CacheEntry
Generating XML output for class vg::CactusSide
Generating XML output for class vg::CactusSnarlFinder
Generating XML output for class vg::SnarlCaller::CallInfo
Generating XML output for class vg::MinimumDistanceIndex::ChainIndex
Generating XML output for class vg::ChainIterator
Generating XML output for class vg::SnarlSeedClusterer::Cluster
Generating XML output for class vg::Colors
Generating XML output for class vg::CompletedTranscriptPath
Generating XML output for class vg::ComponentMinDistanceClusterer
Generating XML output for class vg::Configurable
Generating XML output for class vg::ConfigurableParser
Generating XML output for class vg::Connection
Generating XML output for class vg::connection_t
Generating XML output for class vg::ConsistencyCalculator
Generating XML output for class vg::ConstructedChunk
Generating XML output for class vg::Constructor
Generating XML output for class vg::io::ConvertedHashGraph
Generating XML output for class vg::Counts
Generating XML output for class vg::DagifiedGraph
Generating XML output for class vg::Deconstructor
Generating XML output for class vg::BandedGlobalAligner::AltTracebackStack::Deflection
Generating XML output for class handlegraph::DeletableHandleGraph
Generating XML output f/build/vg-t08NLS/vg-1.30.0+ds/src/filter.cpp:939: warning: Unsupported xml/html tag <PCTID> found
or class vg::DeleteHaplotypeCommand
Generating XML output for class vg::DeletionAligner
Generating XML output for class vg::DepthMap
Generating XML output for class vg::DinucleotideMachine
Generating XML output for class vg::discrete_distribution
Generating XML output for class vg::DistanceHeuristic
Generating XML output for class vg::DozeuInterface
Generating XML output for class vg::DozeuPinningOverlay
Generating XML output for class vg::MEMClusterer::DPScoreComparator
Generating XML output for class vg::Edge
Generating XML output for class vg::EdgePileup
Generating XML output for class vg::Edit
Generating XML output for class vg::edit_t
Generating XML output for class vg::EditedTranscriptPath
Generating XML output for class vg::endianness
Generating XML output for class vg::ExhaustiveTraversalFinder
Generating XML output for class vg::Exon
Generating XML output for class handlegraph::ExpandingOverlayGraph
Generating XML output for class vg::ExtraNodeGraph
Generating XML output for class vg::io::fdinbuf
Generating XML output for class vg::io::fdistream
Generating XML output for class vg::io::fdostream
Generating XML output for class vg::io::fdoutbuf
Generating XML output for class vg::FeatureSet::Feature
Generating XML output for class vg::FeatureSet
Generating XML output for class vg::Filter
Generating XML output for class vg::Funnel::FilterPerformance
Generating XML output for class vg::FixedGenotypePriorCalculator
Generating XML output for class vg::FlowCaller
Generating XML output for class vg::FlowSort
Generating XML output for class vg::FlowTraversalFinder
Generating XML output for class vg::FragmentLengthDistribution
Generating XML output for class vg::FragmentLengthStatistics
Generating XML output for class vg::Funnel
Generating XML output for class vg::io::GafAlignmentEmitter
Generating XML output for class vg::GAFOutputCaller
Generating XML output for class gafkluge::GafRecord
Generating XML output for class gafkluge::GafStep
Generating XML output for class vg::GaplessExtender
Generating XML output for class vg::GaplessExtension
Generating XML output for class haplo::gbwt_thread_t
Generating XML output for class vg::GBWTHandler
Generating XML output for class haplo::GBWTScoreProvider
Generating XML output for class vg::GBWTTraversalFinder
Generating XML output for class vg::GenomeState
Generating XML output for class vg::GenomeStateCommand
Generating XML output for class vg::Genotype
Generating XML output for class vg::GenotypeLikelihoodCalculator
Generating XML output for class vg::GenotypePriorCalculator
Generating XML output for class vg::Genotyper
Generating XML output for class vg::algorithms::GFAFormatError
Generating XML output for class vg::GFFReader
Generating XML output for class vg::GFFRecord
Generating XML output for class vg::Graph
Generating XML output for class vg::DozeuInterface::graph_pos_s
Generating XML output for class vg::GraphCaller
Generating XML output for class vg::GraphSynchronizer
Generating XML output for class vg::GreedyMinDistanceClusterer
Generating XML output for class vg::FlowSort::Growth
Generating XML output for class vg::GSSWAligner
Generating XML output for class handlegraph::handle_t
Generating XML output for class handlegraph::HandleGraph
Generating XML output for class vg::HandleGraphSnarlFinder
Generating XML output for class vg::temp_file::Handler
Generating XML output for class xg::temp_file::Handler
Generating XML output for class haplo::haplo_DP
Generating XML output for class haplo::haplo_DP_column
Generating XML output for class haplo::haplo_DP_rectangle
Generating XML output for class vg::PhasedGenome::Haplotype
Generating XML output for class vg::HaplotypeIndexer
Generating XML output for class vg::PhasedGenome::HaplotypeNode
Generating XML output for class std::hash< const vg::Snarl >
Generating XML output for class std::hash< handlegraph::edge_t >
Generating XML output for class std::hash< handlegraph::handle_t >
Generating XML output for class std::hash< handlegraph::net_handle_t >
Generating XML output for class std::hash< handlegraph::path_handle_t >
Generating XML output for class std::hash< handlegraph::step_handle_t >
Generating XML output for class std::hash< pair< A, B > >
Generating XML output for class std::hash< std::tuple< TT... > >
Generating XML output for class std::hash< vg::NodeSide >
Generating XML output for class std::hash< vg::NodeTraversal >
Generating XML output for class vg::Genotyper::hash_ambiguous_allele_set
Generating XML output for class vg::hash_map
Generating XML output for class vg::hash_map< K *, V >
Generating XML output for class vg::Genotyper::hash_node_traversal
Generating XML output for class vg::Genotyper::hash_oriented_edge
Generating XML output for class vg::hash_set
Generating XML output for class vg::hash_set< K * >
Generating XML output for class haplo::hDP_gbwt_graph_accessor
Generating XML output for class hFILE_backend
Generating XML output for class vg::io::hFILE_cppstream
Generating XML output for class vg::MEMClusterer::HitEdge
Generating XML output for class vg::MEMClusterer::HitGraph
Generating XML output for class vg::MEMClusterer::HitNode
Generating XML output for class vg::Homogenizer
Generating XML output for class vg::HTSAlignmentEmitter
Generating XML output for class vg::HTSWriter
Generating XML output for class vg::IdentityOverlay
Generating XML output for class vg::IDScanner
Generating XML output for class vg::IncrementalSubgraph
Generating XML output for class vg::IncrementIter
Generating XML output for class vg::IndexedVG
Generating XML output for class vg::IndexFile
Generating XML output for class vg::IndexingParameters
Generating XML output for class vg::IndexManager
Generating XML output for class vg::IndexRecipe
Generating XML output for class vg::IndexRegistry
Generating XML output for class vg::InsertHaplotypeCommand
Generating XML output for class vg::InsufficientInputException
Generating XML output for class haplo::int_itvl_t
Generating XML output for class vg::IntegratedSnarlFinder
Generating XML output for class vg::is_instantiation_of
Generating XML output for class vg::is_instantiation_of< Predicate< PredicateArgs... >, Predicate >
Generating XML output for class vg::Funnel::Item
Generating XML output for class handlegraph::PathForEachSocket::iterator
Generating XML output for class vg::PhasedGenome::iterator
Generating XML output for class vg::ShuffledPairs::iterator
Generating XML output for class std::iterator_traits< vg::PhasedGenome::iterator >
Generating XML output for class j2pb_error
Generating XML output for class job_type
Generating XML output for class vg::JoinedSpliceGraph
Generating XML output for class json_autoptr
Generating XML output for class vg::io::JSONStreamHelper
Generating XML output for class vg::algorithms::kmer_t
Generating XML output for class vg::kmer_t
Generating XML output for class vg::KmerMatch
Generating XML output for class vg::KmerPosition
Generating XML output for class vg::LegacyCaller
Generating XML output for class haplo::linear_haplo_structure
Generating XML output for class haplo::LinearScoreProvider
Generating XML output for class haplo::linear_haplo_structure::linearUnrepresentable
Generating XML output for class vg::LocationSupport
Generating XML output for class vg::GraphSynchronizer::Lock
Generating XML output for class vg::Locus
Generating XML output for class vg::Mapper
Generating XML output for class vg::Mapping
Generating XML output for class vg::mapping_t
Generating XML output for class vg::NGSSimulator::MarkovDistribution
Generating XML output for class vg::MaximalExactMatch
Generating XML output for class vg::MCMCCaller
Generating XML output for class vg::MCMCGenotyper
Generating XML output for class vg::MEMChainModel
Generating XML output for class vg::MEMChainModelVertex
Generating XML output for class vg::MEMClusterer
Generating XML output for class vg::MemoizingGraph
Generating XML output for class vg::IntegratedSnarlFinder::MergedAdjacencyGraph
Generating XML output for class vg::io::MessageEmitter
Generating XML output for class vg::io::MessageIterator
Generating XML output for class vg::MinDistanceClusterer
Generating XML output for class vg::MinimizerMapper::Minimizer
Generating XML output for class vg::MinimizerMapper
Generating XML output for class vg::MinimumDistanceIndex
Generating XML output for class vg::MIPayload
Generating XML output for class vg::MSAConverter
Generating XML output for class vg::multipath_alignment_t
Generating XML output for class vg::MultipathAlignment
Generating XML output for class vg::MultipathAlignmentEmitter
Generating XML output for class vg::MultipathAlignmentGraph
Generating XML output for class vg::MultipathMapper
Generating XML output for class vg::MultipathProblem
Generating XML output for class handlegraph::MutableHandleGraph
Generating XML output for class handlegraph::MutablePathDeletableHandleGraph
Generating XML output for class handlegraph::MutablePathHandleGraph
Generating XML output for class handlegraph::MutablePathMutableHandleGraph
Generating XML output for class vg::NameMapper
Generating XML output for class vg::NestedTraversalFinder
Generating XML output for class handlegraph::net_handle_t
Generating XML output for class vg::NetGraph
Generating XML output for class vg::SnarlSeedClusterer::NetgraphNode
Generating XML output for class vg::NGSSimulator
Generating XML output for class vg::NoAlignmentInBandException
Generating XML output for class vg::Node
Generating XML output for class vg::SnarlSeedClusterer::NodeClusters
Generating XML output for class vg::NodePileup
Generating XML output for class vg::NodeSide
Generating XML output for class vg::NodeTraversal
Generating XML output for class vg::normal_distribution
Generating XML output for class vg::io::NullAlignmentEmitter
Generating XML output for class vg::NullClusterer
Generating XML output for class vg::NullMaskingGraph
Generating XML output for class handlegraph::number_bool_packing
Generating XML output for class vg::Option
Generating XML output for class vg::Option< vector< Item >, Parser >
Generating XML output for class vg::OptionInterface
Generating XML output for class vg::OptionValueParser
Generating XML output for class vg::OptionValueParser< vector< Item > >
Generating XML output for class vg::DozeuInterface::OrderedGraph
Generating XML output for class vg::OrientedDistanceClusterer
Generating XML output for class vg::OrientedDistanceMeasurer
Generating XML output for class vg::PackedTraversalSupportFinder
Generating XML output for class vg::Packer
Generating XML output for class vg::Packers
Generating XML output for class vg::pair_hash_map
Generating XML output for class vg::pair_hash_set
Generating XML output for class vg::PairedEndMapper
Generating XML output for class vg::Path
Generating XML output for class handlegraph::path_handle_t
Generating XML output for class vg::path_mapping_t
Generating XML output for class vg::path_t
Generating XML output for class vg::PathBasedTraversalFinder
Generating XML output for class vg::PathBranch
Generating XML output for class vg::PathChunker
Generating XML output for class vg::PathComponentIndex
Generating XML output for class handlegraph::PathForEachSocket
Generating XML output for class handlegraph::PathHandleGraph
Generating XML output for class vg::PathIndex
Generating XML output for class vg::PathNode
Generating XML output for class vg::PathOrientedDistanceMeasurer
Generating XML output for class handlegraph::PathPositionHandleGraph
Generating XML output for class vg::PathRestrictedTraversalFinder
Generating XML output for class vg::Paths
Generating XML output for class vg::PathSubgraph
Generating XML output for class vg::PathSubgraphOverlay
Generating XML output for class vg::PathTraversalFinder
Generating XML output for class vg::PhasedGenome
Generating XML output for class vg::PhaseUnfolder
Generating XML output for class vg::Pictographs
Generating XML output for class vg::Pileup
Generating XML output for class vg::VG::Plan
Generating XML output for class vg::PoissonSupportSnarlCaller::PoissonCallInfo
Generating XML output for class vg::PoissonSupportSnarlCaller
Generating XML output for class vg::Position
Generating XML output for class vg::position_t
Generating XML output for class vg::Posit/build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/deps/vg.proto:267: warning: Unsupported xml/html tag <parentSnarlHash> found
/build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/deps/vg.proto:267: warning: Unsupported xml/html tag <parentSnarlHash> found
ionIDScanner
Generating XML output for class vg::Progressive
Generating XML output for class vg::io::ProtobufEmitter
Generating XML output for class vg::io::ProtobufIterator
Generating XML output for class PruningParameters
Generating XML output for class vg::QualAdjAligner
Generating XML output for class vg::QualAdjXdropAligner
Generating XML output for class vg::Range
Generating XML output for class handlegraph::RankedHandleGraph
Generating XML output for class vg::RareVariantSimplifier
Generating XML output for class vg::RatioSupportSnarlCaller
Generating XML output for class vg::ReadFilter
Generating XML output for class vg::ReadRestrictedTraversalFinder
Generating XML output for class vg::Region
Generating XML output for class vg::RegionExpander
Generating XML output for class vg::io::Registry
Generating XML output for class vg::ReplaceLocalHaplotypeCommand
Generating XML output for class vg::ReplaceSnarlHaplotypeCommand
Generating XML output for class vg::RepresentativeTraversalFinder
Generating XML output for class vg::ReverseGraph
Generating XML output for class haplo::haploMath::RRMemo
Generating XML output for class vg::Sampler
Generating XML output for class haplo::ScoreProvider
Generating XML output for class vg::SnarlSeedClusterer::Seed
Generating XML output for class vg::SeqComplexity
Generating XML output for class handlegraph::Serializable
Generating XML output for class handlegraph::SerializableHandleGraph
Generating XML output for class vg::ShuffledPairs
Generating XML output for class vg::SimpleConsistencyCalculator
Generating XML output for class vg::SimpleTraversalSupportCalculator
Generating XML output for class vg::SmallBitset
Generating XML output for class vg::SmallSnarlSimplifier
Generating XML output for class vg::Snarl
Generating XML output for class vg::SnarlCaller
Generating XML output for class handlegraph::SnarlDecomposition
Generating XML output for class vg::SnarlFinder
Generating XML output for class vg::MinimumDistanceIndex::SnarlIndex
Generating XML output for class vg::SnarlManager
Generating XML output for class vg::SnarlMinDistance
Generating XML output for class vg::SnarlOrientedDistanceMeasurer
Generating XML output for class vg::SnarlManager::SnarlRecord
Generating XML output for class vg::SnarlSeedClusterer
Generating XML output for class vg::SnarlState
Generating XML output for class vg::SnarlTraversal
Generating XML output for class haplo::linear_haplo_structure::SNVvector
Generating XML output for class vg::SourceSinkOverlay
Generating XML output for class vg::SplicedHTSAlignmentEmitter
Generating XML output for class vg::SpliceMotifs
Generating XML output for class vg::SpliceRegion
Generating XML output for class vg::SRPE
Generating XML output for class vg::SSWAligner
Generating XML output for class vg::Funnel::Stage
Generating XML output for class vg::state_hash
Generating XML output for class handlegraph::step_handle_t
Generating XML output for class vg::StrandSplitGraph
Generating XML output for class vg::io::streaminbuf
Generating XML output for class vg::StreamIndex
Generating XML output for class vg::StreamIndexBase
Generating XML output for class vg::io::streamistream
Generating XML output for class vg::io::StreamMultiplexer
Generating XML output for class vg::StreamSorter
Generating XML output for class vg::string_hash_map
Generating XML output for class vg::string_hash_set
Generating XML output for class vg::subcommand::Subcommand
Generating XML output for class vg::SubgraphOverlay
Generating XML output for class handlegraph::algorithms::SubHandleGraph
Generating XML output for class vg::SubHandleGraph
Generating XML output for class vg::Subpath
Generating XML output for class vg::subpath_t
Generating XML output for class vg::Support
Generating XML output for class vg::SupportAugmentedGraph
Generating XML output for class vg::SupportBasedSnarlCaller
Generating XML output for class vg::SupportRestrictedTraversalFinder
Generating XML output for class vg::SurjectingAlignmentEmitter
Generating XML output for class vg::Surjector
Generating XML output for class vg::SwapH/build/vg-t08NLS/vg-1.30.0+ds/src/vg.hpp:894: warning: explicit link request to 'matches' could not be resolved
/build/vg-t08NLS/vg-1.30.0+ds/src/vg.hpp:894: warning: explicit link request to 'mismatches' could not be resolved
/build/vg-t08NLS/vg-1.30.0+ds/src/hts_alignment_emitter.hpp:53: warning: Found unknown command '@SQ'
aplotypesCommand
Generating XML output for class vg::io::Registry::Tables
Generating XML output for class vg::TargetValueSearch
Generating XML output for class vg::Watchdog::thread_state_t
Generating XML output for class vg::TipAnchoredMaxDistance
Generating XML output for class vg::Transcript
Generating XML output for class vg::Transcriptome
Generating XML output for class vg::TranscriptPath
Generating XML output for class vg::Translation
Generating XML output for class vg::Translator
Generating XML output for class vg::TraversalFinder
Generating XML output for class vg::TraversalSupportCalculator
Generating XML output for class vg::TraversalSupportFinder
Generating XML output for class vg::Tree
Generating XML output for class vg::BitStringTree::TreeNode
Generating XML output for class vg::TreeNode
Generating XML output for class vg::SnarlSeedClusterer::TreeState
Generating XML output for class vg::TreeSubgraph
Generating XML output for class handlegraph::TriviallySerializable
Generating XML output for class vg::TrivialTraversalFinder
Generating XML output for class vg::io::TSVAlignmentEmitter
Generating XML output for class vg::TVSClusterer
Generating XML output for class vg::uniform_int_distribution
Generating XML output for class vg::uniform_real_distribution
Generating XML output for class vg::VariantAdder
Generating XML output for class vg::VcfBuffer
Generating XML output for class vg::VCFGenotyper
Generating XML output for class vg::VCFOutputCaller
Generating XML output for class vg::VcfRecordConverter
Generating XML output for class vg::VcfRecordFilter
Generating XML output for class vg::VCFTraversalFinder
Generating XML output for class handlegraph::VectorizableHandleGraph
Generating XML output for class Vectorizer
Generating XML output for class vg::Version
Generating XML output for class vg::VG
Generating XML output for class vg::io::VGAlignmentEmitter
Generating XML output for class vg::VGIndexes
Generating XML output for class vg::VGset
Generating XML output for class vg::Visit
Generating XML output for class vg::Viz
Generating XML output for class vg::io::VPKG
Generating XML output for class vg::algorithms::walk_t
Generating XML output for class vg::wang_hash
Generating XML output for class vg::wang_hash< handle_t >
Generating XML output for class vg::wang_hash< NodeSide >
Generating XML output for class vg::wang_hash< NodeTraversal >
Generating XML output for class vg::wang_hash< path_handle_t >
Generating XML output for class vg::wang_hash< std::pair< A, B > >
Generating XML output for class vg::wang_hash< T * >
Generating XML output for class vg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >
Generating XML output for class vg::Watchdog
Generating XML output for class vg::FlowSort::WeightedGraph
Generating XML output for class vg::WideningPRNG
Generating XML output for class vg::WindowedVcfBuffer
Generating XML output for class vg::WrappingPositionScanner
Generating XML output for class vg::XdropAligner
Generating XML output for class xg::XG
Generating XML output for class xg::XGFormatError
Generating XML output for class xg::XGPath
Generating XML output for namespace @452
Generating XML output for namespace bdsg
Generating XML output for namespace gafkluge
Generating XML output for namespace gfak
Generating XML output for namespace google
Generating XML output for namespace google::protobuf
Generating XML output for namespace google::protobuf::io
Generating XML output for namespace handlegraph
Generating XML output for namespace handlegraph::algorithms
Generating XML output for namespace haplo
Generating XML output for namespace haplo::haploMath
Generating XML output for namespace sdsl
Generating XML output for namespace spp
Generating XML output for namespace std
Generating XML output for namespace std::@79
Generating XML output for namespace structures
Generating XML output for namespace vg
Generating XML output for namespace vg::algorithms
Generating XML output for namespace vg::io
Generating XML output for namespace vg::subcommand
Generating XML output for namespace vg::temp_file
Generating XML output for namespace vg::unittest
Generating XML output for namespace xg
Generating XML output for namespace xg::temp_file
Generating XML output for file append_graph.cpp
Generating XML output for file apply_orientations.cpp
Generating XML output for file are_equivalent.cpp
Generating XML output for file copy_graph.cpp
Generating XML output for file count_walks.cpp
Generating XML output for file dagify.cpp
Generating XML output for file deletable_handle_graph.cpp
Generating XML output for file dijkstra.cpp
Generating XML output for file eades_algorithm.cpp
Generating XML output for file extend.cpp
Generating XML output for file find_shortest_paths.cpp
Generating XML output for file find_tips.cpp
Generating XML output for file handle_graph.cpp
Generating XML output for file buildable_snarl_decomposition.hpp
Generating XML output for file deletable_handle_graph.hpp
Generating XML output for file expanding_overlay_graph.hpp
Generating XML output for file handle_graph.hpp
Generating XML output for file iteratee.hpp
Generating XML output for file mutable_handle_graph.hpp
Generating XML output for file mutable_path_deletable_handle_graph.hpp
Generating XML output for file mutable_path_handle_graph.hpp
Generating XML output for file mutable_path_mutable_handle_graph.hpp
Generating XML output for file path_handle_graph.hpp
Generating XML output for file path_position_handle_graph.hpp
Generating XML output for file serializable.hpp
Generating XML output for file serializable_handle_graph.hpp
Generating XML output for file snarl_decomposition.hpp
Generating XML output for file trivially_serializable.hpp
Generating XML output for file util.hpp
Generating XML output for file is_acyclic.cpp
Generating XML output for file is_single_stranded.cpp
Generating XML output for file mutable_handle_graph.cpp
Generating XML output for file path_handle_graph.cpp
Generating XML output for file path_position_handle_graph.cpp
Generating XML output for file ranked_handle_graph.cpp
Generating XML output for file reverse_complement.cpp
Generating XML output for file serializable.cpp
Generating XML output for file snarl_decomposition.cpp
Generating XML output for file split_strands.cpp
Generating XML output for file strongly_connected_components.cpp
Generating XML output for file topological_sort.cpp
Generating XML output for file trivially_serializable.cpp
Generating XML output for file types.cpp
Generating XML output for file unchop.cpp
Generating XML output for file weakly_connected_components.cpp
Generating XML output for file vg.proto
Generating XML output for file alignment_emitter.hpp
Generating XML output for file alignment_io.hpp
Generating XML output for file basic_stream.hpp
Generating XML output for file blocked_gzip_input_stream.hpp
Generating XML output for file blocked_gzip_output_stream.hpp
Generating XML output for file edit.hpp
Generating XML output for file fdstream.hpp
Generating XML output for file gafkluge.hpp
Generating XML output for file hfile_cppstream.hpp
Generating XML output for file hfile_internal.hpp
Generating XML output for file json2pb.h
Generating XML output for file loader.hpp
Generating XML output for file message_emitter.hpp
Generating XML output for file message_iterator.hpp
Generating XML output for file protobuf_emitter.hpp
Generating XML output for file protobuf_iterator.hpp
Generating XML output for file registry.hpp
Generating XML output for file stream.hpp
Generating XML output for file stream_multiplexer.hpp
Generating XML output for file vpkg.hpp
Generating XML output for file alignment_emitter.cpp
Generating XML output for file alignment_io.cpp
Generating XML output for file basic_stream.cpp
Generating XML output for file bin2ascii.h
Generating XML output for file blocked_gzip_input_stream.cpp
Generating XML output for file blocked_gzip_output_stream.cpp
Generating XML output for file edit.cpp
Generating XML output for file hfile_cppstream.cpp
Generating XML output for file json2pb.cpp
Generating XML output for file message_emitter.cpp
Generating XML output for file message_iterator.cpp
Generating XML output for file registry.cpp
Generating XML output for file stream.cpp
Generating XML output for file stream_multiplexer.cpp
Generating XML output for file vpkg.cpp
Generating XML output for file xg.cpp
Generating XML output for file xg.hpp
Generating XML output for file a_star.hpp
Generating XML output for file alignment_path_offsets.cpp
Generating XML output for file alignment_path_offsets.hpp
Generating XML output for file approx_path_distance.cpp
Generating XML output for file approx_path_distance.hpp
Generating XML output for file coverage_depth.cpp
Generating XML output for file coverage_depth.hpp
Generating XML output for file dfs.cpp
Generating XML output for file dfs.hpp
Generating XML output for file disjoint_components.cpp
Generating XML output for file disjoint_components.hpp
Generating XML output for file distance_to_head.cpp
Generating XML output for file distance_to_head.hpp
Generating XML output for file distance_to_tail.cpp
Generating XML output for file distance_to_tail.hpp
Generating XML output for file expand_context.cpp
Generating XML output for file expand_context.hpp
Generating XML output for file extract_connecting_graph.cpp
Generating XML output for file extract_connecting_graph.hpp
Generating XML output for file extract_containing_graph.cpp
Generating XML output for file extract_containing_graph.hpp
Generating XML output for file extract_extending_graph.cpp
Generating XML output for file extract_extending_graph.hpp
Generating XML output for file gfa_to_handle.cpp
Generating XML output for file gfa_to_handle.hpp
Generating XML output for file id_sort.cpp
Generating XML output for file id_sort.hpp
Generating XML output for file jump_along_path.cpp
Generating XML output for file jump_along_path.hpp
Generating XML output for file k_widest_paths.cpp
Generating XML output for file k_widest_paths.hpp
Generating XML output for file merge.cpp
Generating XML output for file merge.hpp
Generating XML output for file nearest_offsets_in_paths.cpp
Generating XML output for file nearest_offsets_in_paths.hpp
Generating XML output for file next_pos_chars.cpp
Generating XML output for file next_pos_chars.hpp
Generating XML output for file normalize.cpp
Generating XML output for file normalize.hpp
Generating XML output for file path_string.cpp
Generating XML output for file path_string.hpp
Generating XML output for file prune.cpp
Generating XML output for file prune.hpp
Generating XML output for file ref_path_distance.cpp
Generating XML output for file ref_path_distance.hpp
Generating XML output for file shortest_cycle.cpp
Generating XML output for file shortest_cycle.hpp
Generating XML output for file simplify_siblings.cpp
Generating XML output for file simplify_siblings.hpp
Generating XML output for file sorted_id_ranges.cpp
Generating XML output for file sorted_id_ranges.hpp
Generating XML output for file three_edge_connected_components.cpp
Generating XML output for file three_edge_connected_components.hpp
Generating XML output for file to_gfa.cpp
Generating XML output for file to_gfa.hpp
Generating XML output for file walk.cpp
Generating XML output for file walk.hpp
Generating XML output for file aligner.cpp
Generating XML output for file aligner.hpp
Generating XML output for file alignment.cpp
Generating XML output for file alignment.hpp
Generating XML output for file annotation.hpp
Generating XML output for file augment.cpp
Generating XML output for file augment.hpp
Generating XML output for file banded_global_aligner.cpp
Generating XML output for file banded_global_aligner.hpp
Generating XML output for file benchmark.cpp
Generating XML output for file benchmark.hpp
Generating XML output for file build_index.cpp
Generating XML output for file build_index.hpp
Generating XML output for file cactus.cpp
Generating XML output for file cactus.hpp
Generating XML output for file cactus_snarl_finder.cpp
Generating XML output for file cactus_snarl_finder.hpp
Generating XML output for file chunker.cpp
Generating XML output for file chunker.hpp
Generating XML output for file cluster.cpp
Generating XML output for file cluster.hpp
Generating XML output for file colors.hpp
Generating XML output for file constructor.cpp
Generating XML output for file constructor.hpp
Generating XML output for file convert.hpp
Generating XML output for file crash.cpp
Generating XML output for file crash.hpp
Generating XML output for file dagified_graph.cpp
Generating XML output for file dagified_graph.hpp
Generating XML output for file deconstructor.cpp
Generating XML output for file deconstructor.hpp
Generating XML output for file deletion_aligner.cpp
Generating XML output for file deletion_aligner.hpp
Generating XML output for file dinucleotide_machine.cpp
Generating XML output for file dinucleotide_machine.hpp
Generating XML output for file dozeu_interface.cpp
Generating XML output for file dozeu_interface.hpp
Generating XML output for file dozeu_pinning_overlay.cpp
Generating XML output for file dozeu_pinning_overlay.hpp
Generating XML output for file endianness.hpp
Generating XML output for file entropy.cpp
Generating XML output for file entropy.hpp
Generating XML output for file extra_node_graph.cpp
Generating XML output for file extra_node_graph.hpp
Generating XML output for file feature_set.cpp
Generating XML output for file feature_set.hpp
Generating XML output for file filter.cpp
Generating XML output for file filter.hpp
Generating XML output for file flow_sort.cpp
Generating XML output for file flow_sort.hpp
Generating XML output for file funnel.cpp
Generating XML output for file funnel.hpp
Generating XML output for file gapless_extender.cpp
Generating XML output for file gapless_extender.hpp
Generating XML output for file gbwt_helper.cpp
Generating XML output for file gbwt_helper.hpp
Generating XML output for file genome_state.cpp
Generating XML output for file genome_state.hpp
Generating XML output for file genotypekit.cpp
Generating XML output for file genotypekit.hpp
Generating XML output for file genotyper.cpp
Generating XML output for file genotyper.hpp
Generating XML output for file gfa.cpp
Generating XML output for file gfa.hpp
Generating XML output for file gff_reader.cpp
Generating XML output for file gff_reader.hpp
Generating XML output for file graph.cpp
Generating XML output for file graph.hpp
Generating XML output for file graph_caller.cpp
Generating XML output for file graph_caller.hpp
Generating XML output for file graph_synchronizer.cpp
Generating XML output for file graph_synchronizer.hpp
Generating XML output for file handle.hpp
Generating XML output for file haplotype_extracter.cpp
Generating XML output for file haplotype_extracter.hpp
Generating XML output for file haplotype_indexer.cpp
Generating XML output for file haplotype_indexer.hpp
Generating XML output for file haplotypes.cpp
Generating XML output for file haplotypes.hpp
Generating XML output for file hash_map.hpp
Generating XML output for file homogenizer.cpp
Generating XML output for file homogenizer.hpp
Generating XML output for file hts_alignment_emitter.cpp
Generating XML output for file hts_alignment_emitter.hpp
Generating XML output for file identity_overlay.cpp
Generating XML output for file identity_overlay.hpp
Generating XML output for file incremental_subgraph.cpp
Generating XML output for file incremental_subgraph.hpp
Generating XML output for file index_manager.cpp
Generating XML output for file index_manager.hpp
Generating XML output for file index_registry.cpp
Generating XML output for file index_registry.hpp
Generating XML output for file indexed_vg.cpp
Generating XML output for file indexed_vg.hpp
Generating XML output for file integrated_snarl_finder.cpp
Generating XML output for file integrated_snarl_finder.hpp
Generating XML output for file converted_hash_graph.hpp
Generating XML output for file json_stream_helper.hpp
Generating XML output for file load_proto_to_graph.cpp
Generating XML output for file load_proto_to_graph.hpp
Generating XML output for file register_libvg_io.cpp
Generating XML output for file register_libvg_io.hpp
Generating XML output for file register_loader_saver_distance_index.cpp
Generating XML output for file register_loader_saver_distance_index.hpp
Generating XML output for file register_loader_saver_gbwt.cpp
Generating XML output for file register_loader_saver_gbwt.hpp
Generating XML output for file register_loader_saver_gbwtgraph.cpp
Generating XML output for file register_loader_saver_gbwtgraph.hpp
Generating XML output for file register_loader_saver_gcsa.cpp
Generating XML output for file register_loader_saver_gcsa.hpp
Generating XML output for file register_loader_saver_hash_graph.cpp
Generating XML output for file register_loader_saver_hash_graph.hpp
Generating XML output for file register_loader_saver_lcp.cpp
Generating XML output for file register_loader_saver_lcp.hpp
Generating XML output for file register_loader_saver_minimizer.cpp
Generating XML output for file register_loader_saver_minimizer.hpp
Generating XML output for file register_loader_saver_odgi.cpp
Generating XML output for file register_loader_saver_odgi.hpp
Generating XML output for file register_loader_saver_packed_graph.cpp
Generating XML output for file register_loader_saver_packed_graph.hpp
Generating XML output for file register_loader_saver_r_index.cpp
Generating XML output for file register_loader_saver_r_index.hpp
Generating XML output for file register_loader_saver_snarl_manager.cpp
Generating XML output for file register_loader_saver_snarl_manager.hpp
Generating XML output for file register_loader_saver_vg.cpp
Generating XML output for file register_loader_saver_vg.hpp
Generating XML output for file register_loader_saver_xg.cpp
Generating XML output for file register_loader_saver_xg.hpp
Generating XML output for file save_handle_graph.hpp
Generating XML output for file kmer.cpp
Generating XML output for file kmer.cpp
Generating XML output for file kmer.hpp
Generating XML output for file kmer.hpp
Generating XML output for file main.cpp
Generating XML output for file mapper.cpp
Generating XML output for file mapper.hpp
Generating XML output for file mcmc_caller.cpp
Generating XML output for file mcmc_caller.hpp
Generating XML output for file mcmc_genotyper.cpp
Generating XML output for file mcmc_genotyper.hpp
Generating XML output for file mem.cpp
Generating XML output for file mem.hpp
Generating XML output for file memoizing_graph.cpp
Generating XML output for file memoizing_graph.hpp
Generating XML output for file memusage.cpp
Generating XML output for file memusage.hpp
Generating XML output for file min_distance.cpp
Generating XML output for file min_distance.hpp
Generating XML output for file minimizer_mapper.cpp
Generating XML output for file minimizer_mapper.hpp
Generating XML output for file msa_converter.cpp
Generating XML output for file msa_converter.hpp
Generating XML output for file multipath_alignment.cpp
Generating XML output for file multipath_alignment.hpp
Generating XML output for file multipath_alignment_emitter.cpp
Generating XML output for file multipath_alignment_emitter.hpp
Generating XML output for file multipath_alignment_graph.cpp
Generating XML output for file multipath_alignment_graph.hpp
Generating XML output for file multipath_mapper.cpp
Generating XML output for file multipath_mapper.hpp
Generating XML output for file name_mapper.cpp
Generating XML output for file name_mapper.hpp
Generating XML output for file nested_traversal_finder.cpp
Generating XML output for file nested_traversal_finder.hpp
Generating XML output for file nodeside.hpp
Generating XML output for file nodetraversal.hpp
Generating XML output for file null_masking_graph.cpp
Generating XML output for file null_masking_graph.hpp
Generating XML output for file option.cpp
Generating XML output for file option.hpp
Generating XML output for file packer.cpp
Generating XML output for file packer.hpp
Generating XML output for file path.cpp
Generating XML output for file path.hpp
Generating XML output for file path_component_index.cpp
Generating XML output for file path_component_index.hpp
Generating XML output for file path_index.cpp
Generating XML output for file path_index.hpp
Generating XML output for file path_subgraph.cpp
Generating XML output for file path_subgraph.hpp
Generating XML output for file phase_unfolder.cpp
Generating XML output for file phase_unfolder.hpp
Generating XML output for file phased_genome.cpp
Generating XML output for file phased_genome.hpp
Generating XML output for file pictographs.hpp
Generating XML output for file position.cpp
Generating XML output for file position.hpp
Generating XML output for file preflight.cpp
Generating XML output for file preflight.hpp
Generating XML output for file progressive.cpp
Generating XML output for file progressive.hpp
Generating XML output for file qual_adj_xdrop_aligner.cpp
Generating XML output for file rare_variant_simplifier.cpp
Generating XML output for file rare_variant_simplifier.hpp
Generating XML output for file readfilter.cpp
Generating XML output for file readfilter.hpp
Generating XML output for file region.cpp
Generating XML output for file region.hpp
Generating XML output for file region_expander.cpp
Generating XML output for file region_expander.hpp
Generating XML output for file reverse_graph.cpp
Generating XML output for file reverse_graph.hpp
Generating XML output for file sampler.cpp
Generating XML output for file sampler.hpp
Generating XML output for file scanner.cpp
Generating XML output for file scanner.hpp
Generating XML output for file seed_clusterer.cpp
Generating XML output for file seed_clusterer.hpp
Generating XML output for file sequence_complexity.hpp
Generating XML output for file small_bitset.hpp
Generating XML output for file small_snarl_simplifier.cpp
Generating XML output for file small_snarl_simplifier.hpp
Generating XML output for file snarl_caller.cpp
Generating XML output for file snarl_caller.hpp
Generating XML output for file snarls.cpp
Generating XML output for file snarls.hpp
Generating XML output for file source_sink_overlay.cpp
Generating XML output for file source_sink_overlay.hpp
Generating XML output for file splicing.cpp
Generating XML output for file splicing.hpp
Generating XML output for file split_strand_graph.cpp
Generating XML output for file split_strand_graph.hpp
Generating XML output for file srpe.cpp
Generating XML output for file srpe.hpp
Generating XML output for file ssw_aligner.cpp
Generating XML output for file ssw_aligner.hpp
Generating XML output for file statistics.cpp
Generating XML output for file statistics.hpp
Generating XML output for file stream_index.cpp
Generating XML output for file stream_index.hpp
Generating XML output for file stream_sorter.cpp
Generating XML output for file stream_sorter.hpp
Generating XML output for file add_main.cpp
Generating XML output for file align_main.cpp
Generating XML output for file annotate_main.cpp
Generating XML output for file augment_main.cpp
Generating XML output for file autoindex_main.cpp
Generating XML output for file benchmark_main.cpp
Generating XML output for file call_main.cpp
Generating XML output for file chunk_main.cpp
Generating XML output for file circularize_main.cpp
Generating XML output for file cluster_main.cpp
Generating XML output for file combine_main.cpp
Generating XML output for file concat_main.cpp
Generating XML output for file construct_main.cpp
Generating XML output for file convert_main.cpp
Generating XML output for file deconstruct_main.cpp
Generating XML output for file depth_main.cpp
Generating XML output for file dotplot_main.cpp
Generating XML output for file explode_main.cpp
Generating XML output for file filter_main.cpp
Generating XML output for file find_main.cpp
Generating XML output for file gamcompare_main.cpp
Generating XML output for file gampcompare_main.cpp
Generating XML output for file gamsort_main.cpp
Generating XML output for file gbwt_main.cpp
Generating XML output for file genotype_main.cpp
Generating XML output for file giraffe_main.cpp
Generating XML output for file help_main.cpp
Generating XML output for file ids_main.cpp
Generating XML output for file index_main.cpp
Generating XML output for file inject_main.cpp
Generating XML output for file join_main.cpp
Generating XML output for file kmers_main.cpp
Generating XML output for file map_main.cpp
Generating XML output for file mcmc_main.cpp
Generating XML output for file minimizer_main.cpp
Generating XML output for file mod_main.cpp
Generating XML output for file mpmap_main.cpp
Generating XML output for file msga_main.cpp
Generating XML output for file pack_main.cpp
Generating XML output for file paths_main.cpp
Generating XML output for file prune_main.cpp
Generating XML output for file recalibrate_main.cpp
Generating XML output for file rna_main.cpp
Generating XML output for file sift_main.cpp
Generating XML output for file sim_main.cpp
Generating XML output for file simplify_main.cpp
Generating XML output for file snarls_main.cpp
Generating XML output for file sort_main.cpp
Generating XML output for file srpe_main.cpp
Generating XML output for file stats_main.cpp
Generating XML output for file subcommand.cpp
Generating XML output for file subcommand.hpp
Generating XML output for file surject_main.cpp
Generating XML output for file test_main.cpp
Generating XML output for file trace_main.cpp
Generating XML output for file translate_main.cpp
Generating XML output for file validate_main.cpp
Generating XML output for file vectorize_main.cpp
Generating XML output for file version_main.cpp
Generating XML output for file view_main.cpp
Generating XML output for file viz_main.cpp
Generating XML output for file subgraph.cpp
Generating XML output for file subgraph.cpp
Generating XML output for file subgraph.hpp
Generating XML output for file subgraph.hpp
Generating XML output for file subgraph_overlay.cpp
Generating XML output for file subgraph_overlay.hpp
Generating XML output for file surjecting_alignment_emitter.cpp
Generating XML output for file surjecting_alignment_emitter.hpp
Generating XML output for file surjector.cpp
Generating XML output for file surjector.hpp
Generating XML output for file swap_remove.hpp
Generating XML output for file transcriptome.cpp
Generating XML output for file transcriptome.hpp
Generating XML output for file translator.cpp
Generating XML output for file translator.hpp
Generating XML output for file traversal_finder.cpp
Generating XML output for file traversal_finder.hpp
Generating XML output for file traversal_support.cpp
Generating XML output for file traversal_support.hpp
Generating XML output for file tree_subgraph.cpp
Generating XML output for file tree_subgraph.hpp
Generating XML output for file types.hpp
Generating XML output for file types.hpp
Generating XML output for file driver.cpp
Generating XML output for file driver.hpp
Generating XML output for file utility.cpp
Generating XML output for file utility.hpp
Generating XML output for file variant_adder.cpp
Generating XML output for file variant_adder.hpp
Generating XML output for file variant_recall.cpp
Generating XML output for file variant_recall.hpp
Generating XML output for file vcf_buffer.cpp
Generating XML output for file vcf_buffer.hpp
Generating XML output for file vectorizer.cpp
Generating XML output for file vectorizer.hpp
Generating XML output for file version.cpp
Generating XML output for file version.hpp
Generating XML output for file vg.cpp
Generating XML output for file vg.hpp
Generating XML output for file vg_set.cpp
Generating XML output for file vg_set.hpp
Generating XML output for file viz.cpp
Generating XML output for file viz.hpp
Generating XML output for file wang_hash.hpp
Generating XML output for file watchdog.cpp
Generating XML output for file watchdog.hpp
Generating XML output for file xdrop_aligner.cpp
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/src/algorithms/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/deps/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/include/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/src/io/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/io/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/src/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/src/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/src/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/libhandlegraph/src/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/src/subcommand/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/src/unittest/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/libvgio/include/vg/
Generate XML output for dir /build/vg-t08NLS/vg-1.30.0+ds/deps/xg/
Running plantuml with JAVA...
lookup cache used 12549/65536 hits=86853 misses=14307
finished...
echo "View documentation at: file:///build/vg-t08NLS/vg-1.30.0+ds/doc/doxygen/index.html"
View documentation at: file:///build/vg-t08NLS/vg-1.30.0+ds/doc/doxygen/index.html
make[2]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds'
make[1]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds'
   debian/rules override_dh_auto_test-indep
make[1]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds'
echo No arch independent tests
No arch independent tests
make[1]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds'
   create-stamp debian/debhelper-build-stamp
   dh_prep -i
   dh_installdocs -i
   dh_installchangelogs -i
   dh_installman -i
   dh_perl -i
   dh_link -i
   dh_strip_nondeterminism -i
   dh_compress -i
   dh_fixperms -i
   dh_missing -i
   dh_installdeb -i
   debian/rules override_dh_gencontrol
make[1]: Entering directory '/build/vg-t08NLS/vg-1.30.0+ds'
dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-3), "
make[1]: Leaving directory '/build/vg-t08NLS/vg-1.30.0+ds'
   dh_md5sums -i
   dh_builddeb -i
dpkg-deb: building package 'vg-docs' in '../vg-docs_1.30.0+ds-1_all.deb'.
 dpkg-genbuildinfo --build=all
 dpkg-genchanges --build=all >../vg_1.30.0+ds-1_all.changes
dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
I: running special hook: sync-out /build/vg-t08NLS /tmp/vg-1.30.0+ds-1phf0jlws
I: cleaning package lists and apt cache...
I: creating tarball...
I: done
I: removing tempdir /tmp/mmdebstrap.Jvh0JejnHy...
I: success in 867.4115 seconds
md5: vg-docs_1.30.0+ds-1_all.deb: OK
sha1: vg-docs_1.30.0+ds-1_all.deb: OK
sha256: vg-docs_1.30.0+ds-1_all.deb: OK
Checksums: OK