Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/picard-tools/picard-tools_2.27.1+dfsg-1_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/picard-tools-2.27.1+dfsg-1e418iazm/picard-tools_2.27.1+dfsg-1_all.buildinfo Get source package info: picard-tools=2.27.1+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/picard-tools/2.27.1+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.121 ant=1.10.12-1 ant-optional=1.10.12-1 antlr=2.7.7+dfsg-12 autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 bnd=5.0.1-3 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 ca-certificates-java=20190909 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-20 dash=0.5.11+git20210903+057cd650a4ed-8 dctrl-tools=2.24-3+b1 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.1 default-jdk=2:1.11-72 default-jdk-doc=2:1.11-72 default-jdk-headless=2:1.11-72 default-jre=2:1.11-72 default-jre-headless=2:1.11-72 devscripts=2.22.1 dh-autoreconf=20 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dirmngr=2.2.34-1 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 fakeroot=1.28-1 file=1:5.41-3 findutils=4.9.0-3 fontconfig=2.13.1-4.4 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.2.0-20 gcc=4:11.2.0-2 gcc-11=11.2.0-20 gcc-11-base=11.2.0-20 gcc-12-base=12-20220319-1 gettext=0.21-6 gettext-base=0.21-6 gnupg=2.2.34-1 gnupg-l10n=2.2.34-1 gnupg-utils=2.2.34-1 gpg=2.2.34-1 gpg-agent=2.2.34-1 gpg-wks-client=2.2.34-1 gpg-wks-server=2.2.34-1 gpgconf=2.2.34-1 gpgsm=2.2.34-1 gpgv=2.2.34-1 gradle=4.4.1-13 gradle-debian-helper=2.1 grep=3.7-1 groff-base=1.22.4-8 groovy=2.4.21-1 gzip=1.12-1 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 ivy=2.5.0-2 java-common=0.72 java-wrappers=0.3 javahelper=0.78 junit4=4.13.2-1 libacl1=2.3.1-1 libantlr-java=2.7.7+dfsg-12 libaopalliance-java=20070526-6 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-20 libasm-java=9.2-1 libasound2=1.2.6.1-2+b1 libasound2-data=1.2.6.1-2 libassuan0=2.5.5-1 libatinject-jsr330-api-java=1.0+ds1-5 libatomic1=12-20220319-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libavahi-client3=0.8-5 libavahi-common-data=0.8-5 libavahi-common3=0.8-5 libb-hooks-op-check-perl=0.22-1+b4 libbarclay-java=2.1.0-3.1 libbcel-java=6.5.0-1 libbcpg-java=1.68-5 libbcprov-java=1.68-5 libbinutils=2.38-3 libblas3=3.10.1-1 libblkid1=2.38-4 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbsf-java=1:2.4.0-8 libbsh-java=2.0b4-20 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12-20220319-1 libcdi-api-java=1.2-3 libclass-method-modifiers-perl=2.13-1 libclass-xsaccessor-perl=1.19-3+b8 libcom-err2=1.46.5-2 libcommons-cli-java=1.4-2 libcommons-codec-java=1.15-1 libcommons-collections3-java=3.2.2-2 libcommons-collections4-java=4.2-1 libcommons-compress-java=1.21-1 libcommons-io-java=2.11.0-2 libcommons-jexl2-java=2.1.1-5 libcommons-lang-java=2.6-9 libcommons-lang3-java=3.11-1 libcommons-logging-java=1.2-3 libcommons-math3-java=3.6.1-3 libcommons-parent-java=43-1 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libcups2=2.4.1op1-2 libcurl4=7.82.0-2 libdatrie1=0.2.13-2 libdb5.3=5.3.28+dfsg1-0.8 libdbus-1-3=1.14.0-1 libdd-plist-java=1.20-1.1 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdeflate0=1.10-2 libdevel-callchecker-perl=0.008-1+b3 libdom4j-java=2.1.3-1 libdpkg-perl=1.21.7 libdrm-amdgpu1=2.4.110-1 libdrm-common=2.4.110-1 libdrm-nouveau2=2.4.110-1 libdrm-radeon1=2.4.110-1 libdrm2=2.4.110-1 libdynaloader-functions-perl=0.003-1.1 libeclipse-jdt-annotation-java=2.2.600+eclipse4.21-1 libedit2=3.1-20210910-1 libel-api-java=3.0.0-3 libelf1=0.186-1 libencode-locale-perl=1.05-1.1 libexpat1=2.4.8-1 libfakeroot=1.28-1 libfelix-framework-java=4.6.1-2.1 libfelix-gogo-runtime-java=0.16.2-1.1 libfelix-resolver-java=1.16.0-1 libffi8=3.4.2-4 libfile-dirlist-perl=0.05-2 libfile-homedir-perl=1.006-1 libfile-listing-perl=6.15-1 libfile-stripnondeterminism-perl=1.13.0-1 libfile-touch-perl=0.12-1 libfile-which-perl=1.27-1 libfindbugs-java=3.1.0~preview2-3 libfontconfig1=2.13.1-4.4 libfreemarker-java=2.3.23-11 libfreetype6=2.11.1+dfsg-1 libfribidi0=1.0.8-2.1 libgatk-native-bindings-java=1.0.0-2.1 libgcc-11-dev=11.2.0-20 libgcc-s1=12-20220319-1 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgeronimo-annotation-1.3-spec-java=1.3-1 libgeronimo-interceptor-3.0-spec-java=1.0.1-4 libgfortran5=12-20220319-1 libgif7=5.1.9-2.1 libgkl-java=0.8.9+dfsg-4 libgkl-jni=0.8.9+dfsg-4 libgl1=1.4.0-1 libgl1-mesa-dri=22.0.2-1 libglapi-mesa=22.0.2-1 libglib2.0-0=2.72.1-1 libglvnd0=1.4.0-1 libglx-mesa0=22.0.2-1 libglx0=1.4.0-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.4-2 libgomp1=12-20220319-1 libgoogle-gson-java=2.8.8-1 libgpg-error0=1.43-3 libgradle-core-java=4.4.1-13 libgradle-plugins-java=4.4.1-13 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b1 libguava-java=29.0-6 libguice-java=4.2.3-2 libhamcrest-java=1.3-9 libharfbuzz0b=2.7.4-1+b1 libhawtjni-runtime-java=1.17-1 libhogweed6=3.7.3-1 libhtml-parser-perl=3.78-1 libhtml-tagset-perl=3.20-4 libhtml-tree-perl=5.07-2 libhtsjdk-java=2.24.1+dfsg-3 libhtsjdk-java-doc=2.24.1+dfsg-3 libhttp-cookies-perl=6.10-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.36-1 libhttp-negotiate-perl=6.01-1 libhttpclient-java=4.5.13-3 libhttpcore-java=4.4.14-2 libice6=2:1.0.10-1 libicu71=71.1-2 libidn2-0=2.3.2-2 libimport-into-perl=1.002005-1 libio-html-perl=1.004-3 libio-pty-perl=1:1.15-2+b1 libio-socket-ssl-perl=2.074-2 libipc-run-perl=20200505.0-1 libisl23=0.24-2 libitm1=12-20220319-1 libjansi-java=1.18-1 libjansi-native-java=1.8-1 libjarjar-java=1.4+svn142-10 libjatl-java=0.2.3-1.1 libjavaewah-java=1.1.7-1 libjaxen-java=1.1.6-4 libjbig0=2.1-3.1+b2 libjcifs-java=1.3.19-2 libjcip-annotations-java=20060626-6 libjcommander-java=1.71-3 libjetty9-java=9.4.45-1 libjformatstring-java=0.10~20131207-2.1 libjgit-java=4.11.9-1 libjline2-java=2.14.6-4 libjna-java=5.9.0-1 libjna-jni=5.9.0-1 libjoptsimple-java=5.0.4-4 libjpeg62-turbo=1:2.1.2-1 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjsch-java=0.1.55-1 libjson-simple-java=2.3.0-1 libjsoup-java=1.14.3-1 libjsp-api-java=2.3.4-3 libjsr305-java=0.1~+svn49-11 libjzlib-java=1.1.3-2 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 libkryo-java=2.20-7 libksba8=1.6.0-2 liblapack3=3.10.1-1 liblcms2-2=2.12~rc1-2 libldap-2.5-0=2.5.11+dfsg-1 liblightcouch-java=0.0.6-1.1 libllvm14=1:14.0.1-1 liblog4j2-java=2.17.1-1 liblogback-java=1:1.2.11-1 liblsan0=12-20220319-1 liblwp-mediatypes-perl=6.04-1 liblwp-protocol-https-perl=6.10-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-3 libmagic1=1:5.41-3 libmaven-parent-java=31-2 libmaven-resolver-java=1.4.2-3 libmaven-shared-utils-java=3.3.0-1 libmaven3-core-java=3.6.3-5 libmd0=1.0.4-1 libminlog-java=1.3.0-1.1 libmodule-runtime-perl=0.016-1 libmongodb-java=3.6.3-2 libmoo-perl=2.005004-3 libmount1=2.38-4 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libnative-platform-java=0.14-5 libnative-platform-jni=0.14-5 libncurses6=6.3-2 libncursesw6=6.3-2 libnekohtml-java=1.9.22-1.1 libnet-http-perl=6.22-1 libnet-ssleay-perl=1.92-1+b1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libngs-java=2.11.2-3 libngs-sdk-dev=2.11.2-3 libngs-sdk2=2.11.2-3 libnpth0=1.6-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnspr4=2:4.33-1 libnss3=2:3.77-1 libobjenesis-java=3.2-1 libosgi-annotation-java=8.0.1-1 libosgi-compendium-java=7.0.0-1 libosgi-core-java=7.0.0-2 libp11-kit0=0.24.1-1 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpango-1.0-0=1.50.6+ds-2 libpangocairo-1.0-0=1.50.6+ds-2 libpangoft2-1.0-0=1.50.6+ds-2 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libparams-classify-perl=0.015-1+b4 libpcre2-8-0=10.39-4 libpcre3=2:8.39-14 libpcsclite1=1.9.5-3 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libpixman-1-0=0.40.0-1 libplexus-cipher-java=1.8-2 libplexus-classworlds-java=2.6.0-1 libplexus-component-annotations-java=2.1.0-1 libplexus-container-default-java=2.1.0-1 libplexus-interpolation-java=1.26-1 libplexus-sec-dispatcher-java=1.4-4 libplexus-utils2-java=3.3.0-1 libpng16-16=1.6.37-4 libpolyglot-maven-java=0.8~tobrien+git20120905-10 libpsl5=0.21.0-1.2 libpython3-stdlib=3.10.4-1 libpython3.10-minimal=3.10.4-3 libpython3.10-stdlib=3.10.4-3 libqdox-java=1.12.1-3 libquadmath0=12-20220319-1 libreadline8=8.1.2-1.2 libreflectasm-java=1.11.6+dfsg-1 librhino-java=1.7.7.2-3 librole-tiny-perl=2.002004-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-4 libsasl2-modules-db=2.1.28+dfsg-4 libseccomp2=2.5.3-2 libselinux1=3.3-1+b2 libsemanage-common=3.3-1 libsemanage2=3.3-1+b2 libsensors-config=1:3.6.0-7 libsensors5=1:3.6.0-7 libsepol2=3.3-1 libservlet-api-java=4.0.1-2 libservlet3.1-java=1:4.0.1-2 libsigsegv2=2.14-1 libsimple-http-java=4.1.21-1.1 libsisu-inject-java=0.3.4-2 libsisu-plexus-java=0.3.4-3 libslf4j-java=1.7.32-1 libsm6=2:1.2.3-1 libsmartcols1=2.38-4 libsnappy-java=1.1.8.3-1 libsnappy-jni=1.1.8.3-1 libsnappy1v5=1.1.8-1 libsqlite3-0=3.38.2-1 libssh2-1=1.10.0-3 libssl1.1=1.1.1n-1 libstdc++-11-dev=11.2.0-20 libstdc++6=12-20220319-1 libsub-override-perl=0.09-2 libsub-quote-perl=2.006006-1 libsystemd0=250.4-1 libtasn1-6=4.18.0-4 libtcl8.6=8.6.12+dfsg-1 libthai-data=0.1.29-1 libthai0=0.1.29-1 libtiff5=4.3.0-6 libtimedate-perl=2.3300-2 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtk8.6=8.6.12-1 libtool=2.4.7-3 libtry-tiny-perl=0.31-1 libtsan0=11.2.0-20 libubsan1=12-20220319-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 liburi-perl=5.10-1 libuuid1=2.38-4 libvulkan1=1.3.204.1-2 libwagon-file-java=3.3.4-1 libwagon-http-java=3.3.4-1 libwagon-provider-api-java=3.3.4-1 libwebp7=1.2.2-2+b1 libwebsocket-api-java=1.1-2 libwww-perl=6.62-1 libwww-robotrules-perl=6.02-1 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libx11-xcb1=2:1.7.5-1 libxau6=1:1.0.9-1 libxbean-reflect-java=4.5-8 libxcb-dri2-0=1.14-3 libxcb-dri3-0=1.14-3 libxcb-glx0=1.14-3 libxcb-present0=1.14-3 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb-sync1=1.14-3 libxcb-xfixes0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxerces2-java=2.12.1-1 libxext6=2:1.3.4-1 libxfixes3=1:6.0.0-1 libxft2=2.3.4-1 libxi6=2:1.8-1 libxml-commons-external-java=1.4.01-5 libxml-commons-resolver1.1-java=1.2-11 libxml2=2.9.13+dfsg-1+b1 libxpp3-java=1.1.4c-3 libxrender1=1:0.9.10-1 libxshmfence1=1.3-1 libxss1=1:1.2.3-1 libxstream-java=1.4.18-2 libxt6=1:1.2.1-1 libxtst6=2:1.2.3-1 libxxf86vm1=1:1.1.4-1+b2 libxz-java=1.9-1 libyaml-snake-java=1.29-1 libz3-4=4.8.12-1+b1 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.17.3-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 maven-repo-helper=1.10 mawk=1.3.4.20200120-3+b1 media-types=7.1.0 ncurses-base=6.3-2 ncurses-bin=6.3-2 netbase=6.3 openjdk-11-doc=11.0.14.1+1-1 openjdk-11-jdk=11.0.14.1+1-1 openjdk-11-jdk-headless=11.0.14.1+1-1 openjdk-11-jre=11.0.14.1+1-1 openjdk-11-jre-headless=11.0.14.1+1-1 openssl=1.1.1n-1 passwd=1:4.11.1+dfsg1-2 patch=2.7.6-7 patchutils=0.4.2-1 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 perl-openssl-defaults=5 pinentry-curses=1.1.0-4 po-debconf=1.0.21+nmu1 python3=3.10.4-1 python3-minimal=3.10.4-1 python3.10=3.10.4-3 python3.10-minimal=3.10.4-3 r-base-core=4.2.0-1+b1 readline-common=8.1.2-1.2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.03-1 tar=1.34+dfsg-1 testng=6.9.12-4 tzdata=2022a-1 ucf=3.0043 unzip=6.0-26 util-linux=2.38-4 util-linux-extra=2.38-4 wdiff=1.2.2-2+b1 x11-common=1:7.7+23 xdg-utils=1.1.3-4.1 xz-utils=5.2.5-2.1 zip=3.0-12 zlib1g=1:1.2.11.dfsg-4 --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/20220426T025843Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220426T025843Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220425T152932Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220421T205851Z/ 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 picard-tools=2.27.1+dfsg-1 && mkdir -p /build/picard-tools-BIO3c2 && dpkg-source --no-check -x /*.dsc /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg && chown -R builduser:builduser /build/picard-tools-BIO3c2" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1650777078" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/picard-tools-BIO3c2 /tmp/picard-tools-2.27.1+dfsg-1e418iazm bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220421T205851Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.FC3tULMeW0 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.FC3tULMeW0 Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220421T205851Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220421T205851Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (926 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4703 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... 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/20220426T025843Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220426T025843Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220425T152932Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220421T205851Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.FC3tULMeW0 Get:1 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm InRelease [130 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220425T152932Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220421T205851Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm/main Sources [12.0 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm/main amd64 Packages [11.4 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220425T152932Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220425T152932Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220425T152932Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220425T152932Z unstable/main amd64 Packages [12.4 MB] Fetched 36.1 MB in 30s (1200 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.FC3tULMeW0 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d picard-tools=2.27.1+dfsg-1 && mkdir -p /build/picard-tools-BIO3c2 && dpkg-source --no-check -x /*.dsc /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg && chown -R builduser:builduser /build/picard-tools-BIO3c2"' exec /tmp/mmdebstrap.FC3tULMeW0 Reading package lists... NOTICE: 'picard-tools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/picard-tools.git Please use: git clone https://salsa.debian.org/med-team/picard-tools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 19.6 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm/main picard-tools 2.27.1+dfsg-1 (dsc) [2759 B] Get:2 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm/main picard-tools 2.27.1+dfsg-1 (tar) [19.6 MB] Get:3 http://snapshot.notset.fr/archive/debian/20220426T025843Z bookworm/main picard-tools 2.27.1+dfsg-1 (diff) [20.1 kB] Fetched 19.6 MB in 15s (1277 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'picard-tools_2.27.1+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting picard-tools in /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg dpkg-source: info: unpacking picard-tools_2.27.1+dfsg.orig.tar.xz dpkg-source: info: unpacking picard-tools_2.27.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 10-build.xml.patch dpkg-source: info: applying 20-shadowjar.patch dpkg-source: info: applying 30-tests-fix-dataprovider.patch dpkg-source: info: applying 40-tests-fix-testng.patch dpkg-source: info: applying 50-tests-exclude-Barclay.patch dpkg-source: info: applying remove_google_nio.patch dpkg-source: info: applying fix_unreadabletests.patch dpkg-source: info: applying 60-tests-exclude-network.patch dpkg-source: info: applying non-intel-skip-intel-tests dpkg-source: info: applying correct_dataprovider_TestDontMergeAbuttingData.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1650777078" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.FC3tULMeW0 dpkg-buildpackage: info: source package picard-tools dpkg-buildpackage: info: source version 2.27.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . debian/rules clean dh clean --buildsystem=gradle --with javahelper,jh_maven_repo_helper dh_auto_clean -O--buildsystem=gradle install -d /build/picard-tools-BIO3c2/picard-tools-2.27.1\+dfsg/debian/.debhelper/generated/_source/home sh -c "find . -wholename .*build/tmp | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" rm -Rf /build/picard-tools-BIO3c2/picard-tools-2.27.1\+dfsg/.gradle /build/picard-tools-BIO3c2/picard-tools-2.27.1\+dfsg/buildSrc/.gradle .m2 dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* rm -fr debian/.eclipse-build rm -f debian/orbitdeps.debhelper mh_clean -O--buildsystem=gradle debian/rules override_dh_clean make[1]: Entering directory '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/picard-tools.substvars debian/libpicard-java.substvars debian/libpicard-java-doc.substvars debian/files rm -fr -- debian/picard-tools/ debian/tmp/ debian/libpicard-java/ debian/libpicard-java-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) # also remove bai files that are left after tests # find testdata -iname "*.bai" -exec rm {} \; # This needs to be more fine grained since testdata/picard/indices/index_test_b.bam.bai needs to stay! rm -f debian/bd-temp-substvars rm -f debian/bd.substvars make[1]: Leaving directory '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg' debian/rules binary-indep dh binary-indep --buildsystem=gradle --with javahelper,jh_maven_repo_helper dh_update_autotools_config -i -O--buildsystem=gradle dh_autoreconf -i -O--buildsystem=gradle dh_auto_configure -i -O--buildsystem=gradle install -d /build/picard-tools-BIO3c2/picard-tools-2.27.1\+dfsg/debian/.debhelper/generated/_source/home jh_linkjars -i -O--buildsystem=gradle debian/rules override_dh_auto_build make[1]: Entering directory '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg' blhc: ignore-line-regexp: .*gradle.*ScriptTransformer.* dh_auto_build -- jar javadoc mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=picard-tools -Dfile.encoding=UTF-8 --parallel --max-workers=10 jar javadoc Initialized native services in: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/native Using 10 worker leases. Creating new cache for fileHashes, path /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@10fde30a Creating new cache for resourceHashesCache, path /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@10fde30a Creating new cache for fileHashes, path /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@77cf3f8b WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access using Lookup on org.gradle.internal.reflect.JavaMethod (file:/usr/share/gradle/lib/gradle-base-services-4.4.1.jar) to class java.lang.ClassLoader WARNING: Please consider reporting this to the maintainers of org.gradle.internal.reflect.JavaMethod WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release Starting Build Compiling initialization script '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. Creating new cache for metadata-1.1/results, path /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@3b1dc579 Compiling initialization script '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/settings.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/build.gradle'. Included projects: [root project 'picard'] Keep-alive timer started Adding Debian repository to project 'picard' Parallel execution is an incubating feature. Evaluating root project 'picard' using build file '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/build.gradle'. Compiling build file '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/build.gradle' using SubsetScriptTransformer. Compiling build file '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/build.gradle' using BuildScriptTransformer. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg Command: dpkg-parsechangelog -S Version Successfully started process 'command 'dpkg-parsechangelog'' build for version:2.27.1 Creating new cache for metadata-2.36/module-metadata, path /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@1c459c28 Loading the Maven rules... Replacing com.intel.gkl:gkl:jar:0.8.8 -> com.intel.gkl:gkl:jar:debian Replacing com.google.guava:guava:jar:15.0 -> com.google.guava:guava:jar:debian Passing through com.google.guava:guava-parent:jar:debian Passing through commons-io:commons-io:jar:debian Passing through org.apache.commons:commons-parent:jar:debian Passing through org.apache:apache:jar:debian Replacing org.apache.commons:commons-math3:jar:3.5 -> org.apache.commons:commons-math3:jar:debian Replacing org.apache.commons:commons-collections4:jar:4.3 -> org.apache.commons:commons-collections4:jar:debian Replacing commons-lang:commons-lang:jar:2.6 -> commons-lang:commons-lang:jar:debian Replacing com.github.samtools:htsjdk:jar:2.24.1 -> com.github.samtools:htsjdk:jar:debian Replacing org.broadinstitute:barclay:jar:4.0.2 -> org.broadinstitute:barclay:jar:debian Replacing org.apache.logging.log4j:log4j-api:jar:2.17.1 -> org.apache.logging.log4j:log4j-api:jar:debian Passing through org.apache.logging.log4j:log4j:jar:debian Replacing org.apache.logging.log4j:log4j-core:jar:2.17.1 -> org.apache.logging.log4j:log4j-core:jar:debian Passing through org.apache.commons:commons-lang3:jar:debian Passing through org.broadinstitute:gatk-native-bindings:jar:debian Passing through org.jsr-305:jsr305:jar:0.x Passing through org.apache.commons:commons-jexl:jar:debian Passing through commons-logging:commons-logging:jar:debian Passing through org.xerial.snappy:snappy-java:jar:debian Passing through org.apache.commons:commons-compress:jar:debian Passing through org.tukaani:xz:jar:debian Passing through gov.nih.nlm.ncbi:ngs-java:jar:debian Passing through net.sf.jopt-simple:jopt-simple:jar:debian Passing through com.google.code.gson:gson:jar:debian Passing through com.google.code.gson:gson-parent:jar:debian Passing through org.freemarker:freemarker:jar:debian Adding Maven pom generation to project 'picard' Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' from project : Creating new cache for annotation-processors, path /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@744f0e0b Selected primary task 'javadoc' from project : Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar', task ':javadoc'] Creating new cache for resourceHashesCache, path /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@77cf3f8b Creating new cache for taskHistory, path /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@29d563bd Creating new cache for outputFiles, path /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@2dfd157b :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.009 secs. Up-to-date check for task ':compileJava' took 2.758 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. Compiling with JDK Java compiler API. /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:3: warning: [removal] FieldDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.FieldDoc; ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:3: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.ClassDoc; ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:4: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.RootDoc; ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:3: warning: [removal] FieldDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.FieldDoc; ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:3: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.ClassDoc; ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:4: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.RootDoc; ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:3: warning: [removal] FieldDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.FieldDoc; ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:3: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.ClassDoc; ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:4: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.RootDoc; ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:82: warning: [removal] FieldDoc in com.sun.javadoc has been deprecated and marked for removal final FieldDoc[] fieldDocs = currentWorkUnit.getClassDoc().fields(false); ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:83: warning: [removal] FieldDoc in com.sun.javadoc has been deprecated and marked for removal for (final FieldDoc fd : fieldDocs) { ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:32: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal public static boolean start(final RootDoc rootDoc) throws IOException { ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:32: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal public static boolean start(final RootDoc rootDoc) throws IOException { ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:32: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal public static boolean start(final RootDoc rootDoc) throws IOException { ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:58: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal final ClassDoc classDoc, ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:58: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal final ClassDoc classDoc, ^ /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:58: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal final ClassDoc classDoc, ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 17 warnings :compileJava (Thread[Task worker for ':',5,main]) completed. Took 28.001 secs. :processResources (Thread[Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. Up-to-date check for task ':processResources' took 0.026 secs. It is not up-to-date because: No history is available. :processResources (Thread[Task worker for ':',5,main]) completed. Took 0.117 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes (Thread[Task worker for ':',5,main]) completed. Took 0.001 secs. :debianMavenPom (Thread[Task worker for ':',5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.002 secs. It is not up-to-date because: No history is available. Generating pom file /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/build/debian/picard.pom :debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.082 secs. :jar (Thread[Task worker for ':',5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. Up-to-date check for task ':jar' took 0.05 secs. It is not up-to-date because: No history is available. :jar (Thread[Task worker for ':',5,main]) completed. Took 1.253 secs. :javadoc (Thread[Task worker for ':',5,main]) started. :javadoc Putting task artifact state for task ':javadoc' into context took 0.0 secs. Up-to-date check for task ':javadoc' took 0.057 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc''. Working directory: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc @/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/build/tmp/javadoc/javadoc.options Successfully started process 'command '/usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc'' /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java:62: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java:64: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java:68: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:56: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:189: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:189: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:196: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:196: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:189: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:189: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:196: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:196: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:74: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:77: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:80: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:74: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:77: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:80: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/RrbsSummaryMetrics.java:42: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/RrbsSummaryMetrics.java:42: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/RrbsSummaryMetrics.java:42: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/RrbsSummaryMetrics.java:42: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/artifacts/ErrorSummaryMetrics.java:12: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/artifacts/ErrorSummaryMetrics.java:12: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/artifacts/ErrorSummaryMetrics.java:12: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:90: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:91: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:91: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:25: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:25: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:26: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:26: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:152: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:160: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:55: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:58: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:52: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:52: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:55: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:58: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:152: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:154: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:155: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:160: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:162: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:163: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:192: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:192: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:192: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:192: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:982: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:982: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:181: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:291: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:230: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:305: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:246: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:181: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:230: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:246: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:291: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:305: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintMetrics.java:65: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/fingerprint/FingerprintMetrics.java:65: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/BasecallsConverterBuilder.java:177: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java:71: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/IlluminaPhasingMetrics.java:55: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/IlluminaPhasingMetrics.java:55: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/markduplicates/EstimateLibraryComplexity.java:76: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/markduplicates/MarkDuplicates.java:128: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/markduplicates/MarkDuplicates.java:128: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java:280: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java:280: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:112: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:113: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:113: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:114: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:118: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:127: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/Tile.java:38: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/TileMetricsUtil.java:141: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/TileMetricsUtil.java:142: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/pedigree/PedFile.java:19: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/quality/CollectHiSeqXPfFailMetrics.java:386: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/quality/CollectHiSeqXPfFailMetrics.java:389: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/readers/CbclReader.java:37: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/readers/ClocsFileReader.java:57: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/readers/ClocsFileReader.java:57: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/readers/ClocsFileReader.java:57: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/readers/TileMetricsOutReader.java:150: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/illumina/parser/readers/TileMetricsOutReader.java:150: warning - invalid usage of tag & /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:775: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:776: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:778: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:779: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:781: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:782: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:785: warning - invalid usage of tag < /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:786: warning - invalid usage of tag > /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:788: warning - invalid usage of tag < 100 warnings :javadoc (Thread[Task worker for ':',5,main]) completed. Took 11.906 secs. BUILD SUCCESSFUL in 49s 5 actionable tasks: 5 executed make[1]: Leaving directory '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg' jh_build -i -O--buildsystem=gradle create-stamp debian/debhelper-build-stamp dh_testroot -i -O--buildsystem=gradle dh_prep -i -O--buildsystem=gradle rm -f -- debian/picard-tools.substvars debian/libpicard-java.substvars debian/libpicard-java-doc.substvars rm -fr -- debian/.debhelper/generated/picard-tools/ debian/picard-tools/ debian/tmp/ debian/.debhelper/generated/libpicard-java/ debian/libpicard-java/ debian/.debhelper/generated/libpicard-java-doc/ debian/libpicard-java-doc/ dh_auto_install -i -O--buildsystem=gradle install -d /build/picard-tools-BIO3c2/picard-tools-2.27.1\+dfsg/debian/tmp dh_install -i -O--buildsystem=gradle install -d debian/picard-tools/usr/bin cp --reflink=auto -a ./debian/bin/PicardCommandLine debian/picard-tools/usr/bin/ install -d debian/.debhelper/generated/picard-tools install -d debian/.debhelper/generated/libpicard-java install -d debian/.debhelper/generated/libpicard-java-doc jh_installjavadoc -i -O--buildsystem=gradle Installing javadoc from build/docs/javadoc into package libpicard-java-doc install -d debian/libpicard-java-doc/usr/share/doc/libpicard-java cp -r build/docs/javadoc debian/libpicard-java-doc/usr/share/doc/libpicard-java/api cat > debian/libpicard-java-doc.doc-base.javadoc dh_installdocs -i -O--buildsystem=gradle install -d debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./testdata/picard/sam/unmapped.sam debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./testdata/picard/vcf/mini.vcf debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./testdata/picard/vcf/mini.vcf.idx debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./debian/README.test debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./debian/tests/run-unit-test debian/picard-tools/usr/share/doc/picard-tools chmod -R u\+rw,go=rX debian/picard-tools/usr/share/doc install -p -m0644 debian/copyright debian/picard-tools/usr/share/doc/picard-tools/copyright install -d debian/libpicard-java/usr/share/doc/libpicard-java install -p -m0644 debian/copyright debian/libpicard-java/usr/share/doc/libpicard-java/copyright install -d debian/libpicard-java-doc/usr/share/doc/libpicard-java-doc install -p -m0644 debian/copyright debian/libpicard-java-doc/usr/share/doc/libpicard-java-doc/copyright install -d debian/libpicard-java-doc/usr/share/doc-base/ install -p -m0644 debian/libpicard-java-doc.doc-base.javadoc debian/libpicard-java-doc/usr/share/doc-base/libpicard-java-doc.libpicard-java-doc dh_installchangelogs -i -O--buildsystem=gradle install -p -m0644 debian/changelog debian/libpicard-java-doc/usr/share/doc/libpicard-java-doc/changelog.Debian install -p -m0644 debian/changelog debian/libpicard-java/usr/share/doc/libpicard-java/changelog.Debian install -p -m0644 debian/changelog debian/picard-tools/usr/share/doc/picard-tools/changelog.Debian dh_installman -i -O--buildsystem=gradle install -d debian/picard-tools/usr/share/man/man1/ install -p -m0644 ./debian/PicardCommandLine.1 debian/picard-tools/usr/share/man/man1/PicardCommandLine.1 man-recode --to-code UTF-8 --suffix .dh-new debian/picard-tools/usr/share/man/man1/PicardCommandLine.1 mv debian/picard-tools/usr/share/man/man1/PicardCommandLine.1.dh-new debian/picard-tools/usr/share/man/man1/PicardCommandLine.1 chmod 0644 -- debian/picard-tools/usr/share/man/man1/PicardCommandLine.1 dh_installsystemduser -i -O--buildsystem=gradle dh_lintian -i -O--buildsystem=gradle install -d debian/libpicard-java-doc/usr/share/lintian/overrides install -p -m0644 debian/libpicard-java-doc.lintian-overrides debian/libpicard-java-doc/usr/share/lintian/overrides/libpicard-java-doc dh_perl -i -O--buildsystem=gradle rm -f debian/libpicard-java-doc.debhelper.log debian/libpicard-java.debhelper.log debian/picard-tools.debhelper.log debian/rules override_dh_link make[1]: Entering directory '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg' rm -f debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/external/jquery/jquery.js dh_link install -d debian/picard-tools/usr/share/debian-med/bin rm -f debian/picard-tools/usr/share/debian-med/bin/picard ln -s ../../../bin/PicardCommandLine debian/picard-tools/usr/share/debian-med/bin/picard rm -f debian/picard-tools/usr/share/man/man1/picard-tools.1 ln -s PicardCommandLine.1 debian/picard-tools/usr/share/man/man1/picard-tools.1 rm -f debian/picard-tools/usr/bin/picard-tools ln -s PicardCommandLine debian/picard-tools/usr/bin/picard-tools rm -f debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/external/jquery/jquery.js ln -s ../../../../../../javascript/jquery/jquery.min.js debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/external/jquery/jquery.js make[1]: Leaving directory '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg' jh_installlibs -i -O--buildsystem=gradle install -d debian/libpicard-java/usr/share/java install -p -m0644 ./build/libs/picard-2.27.1.jar debian/libpicard-java/usr/share/java/picard-2.27.1.jar rm -f debian/libpicard-java/usr/share/java/picard.jar ln -s picard-2.27.1.jar debian/libpicard-java/usr/share/java/picard.jar jh_classpath -i -O--buildsystem=gradle jh_manifest -i -O--buildsystem=gradle find debian/picard-tools -name '*.jar' find debian/libpicard-java -name '*.jar' Found usr/share/java/picard-2.27.1.jar Found symlink usr/share/java/picard.jar Updating symlinked /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.27.1.jar (using manifest for usr/share/java/picard.jar) Reading manifest from /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.27.1.jar Updating manifest in /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.27.1.jar find debian/libpicard-java-doc -name '*.jar' jh_exec -i -O--buildsystem=gradle jh_depends -i -O--buildsystem=gradle Searching /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/picard-tools for picard-tools Searching Found Jars: Found Debs: Adding substvars: java:Depends= java:Recommends= Searching /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java for libpicard-java Searching /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.27.1.jar Found Jars: /usr/share/java/barclay.jar /usr/share/java/commons-collections4.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-lang3.jar /usr/share/java/commons-math3.jar /usr/share/java/gkl.jar /usr/share/java/guava.jar /usr/share/java/htsjdk.jar /usr/share/java/joptsimple.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/picard-tools/usr/share/java/barclay-2.1.0.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/barclay-2.1.0.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java-doc/usr/share/java/barclay-2.1.0.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/picard-tools/usr/share/java/commons-collections4.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/commons-collections4.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java-doc/usr/share/java/commons-collections4.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/picard-tools/usr/share/java/commons-io.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/commons-io.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java-doc/usr/share/java/commons-io.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/picard-tools/usr/share/java/commons-lang-2.6.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/commons-lang-2.6.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java-doc/usr/share/java/commons-lang-2.6.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/picard-tools/usr/share/java/commons-lang3.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/commons-lang3.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java-doc/usr/share/java/commons-lang3.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/picard-tools/usr/share/java/commons-math3.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/commons-math3.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java-doc/usr/share/java/commons-math3.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/picard-tools/usr/share/java/gkl-0.8.9.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/gkl-0.8.9.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java-doc/usr/share/java/gkl-0.8.9.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/picard-tools/usr/share/java/guava.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/guava.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java-doc/usr/share/java/guava.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/picard-tools/usr/share/java/htsjdk-2.24.1.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/htsjdk-2.24.1.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java-doc/usr/share/java/htsjdk-2.24.1.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/picard-tools/usr/share/java/joptsimple.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java/usr/share/java/joptsimple.jar Checking: /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java-doc/usr/share/java/joptsimple.jar Found Debs: libbarclay-java libcommons-collections4-java libcommons-io-java libcommons-lang-java libcommons-lang3-java libcommons-math3-java libgkl-java libguava-java libhtsjdk-java libjoptsimple-java Adding substvars: java:Depends=libbarclay-java, libcommons-collections4-java, libcommons-io-java, libcommons-lang-java, libcommons-lang3-java, libcommons-math3-java, libgkl-java, libguava-java, libhtsjdk-java, libjoptsimple-java java:Recommends= Searching /build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg/debian/libpicard-java-doc for libpicard-java-doc Searching Found Jars: Found Debs: Adding substvars: java:Depends= java:Recommends= mh_installpoms -i -O--buildsystem=gradle mh_linkjars --skip-clean-poms -i -O--buildsystem=gradle dh_strip_nondeterminism -i -O--buildsystem=gradle Using 1650777078 as canonical time Normalizing debian/libpicard-java/usr/share/java/picard-2.27.1.jar using File::StripNondeterminism::handlers::jar Using 1650777078 as canonical time Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/AbstractIlluminaPositionFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/AbstractIlluminaPositionFileReader.PositionInfo.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/BarcodeFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/BaseBclReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/BaseBclReader.CycleData.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/BaseBclReader.TileData.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/BclIndexReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/BclQualityEvaluationStrategy.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/BclReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/CbclReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/ClocsFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/EmpiricalPhasingMetricsOutReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/FilterFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/LocsFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/MMapBackedIteratorFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/PosFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/TileMetricsOutReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/TileMetricsOutReader.IlluminaLaneTileCode.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/TileMetricsOutReader.IlluminaTileMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/TileMetricsOutReader.TileMetricsVersion.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/quality/CollectHiSeqXPfFailMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/quality/CollectHiSeqXPfFailMetrics.PFFailDetailedMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/quality/CollectHiSeqXPfFailMetrics.PFFailSummaryMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/quality/CollectHiSeqXPfFailMetrics.ReadClassifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/quality/CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/quality/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/quality/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/metrics/GcBiasMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/metrics/MultiLevelCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/metrics/MultilevelMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/metrics/PerUnitMetricCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/metrics/SAMRecordAndReference.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/metrics/SAMRecordAndReferenceMultiLevelCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/metrics/SAMRecordMultiLevelCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/metrics/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/nio/PathProvider.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/nio/PicardHtsPath.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/nio/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/nio/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/pedigree/PedFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/pedigree/PedFile.PedTrio.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/pedigree/Sex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/pedigree/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/pedigree/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fastq/BamToBfq.html using File::StripNonde Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/LiftoverVcf.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/MakeSitesOnlyVcf.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/MakeVcfSampleNameMap.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/MergeVcfs.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/AccumulateVariantCallingMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/ByIntervalListVariantContextIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/CallingMetricAccumulator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/MendelianViolations/FindMendelianViolations.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/MendelianViolations/MendelianViolationMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/MendelianViolations/MendelianViolationsByFamily.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/MendelianViolations/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/MendelianViolations/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VariantAccumulatorExecutor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VariantAccumulatorExecutor.MultiThreadedChunkBased.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VariantIteratorProducer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VariantProcessor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VariantProcessor.Accumulator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VariantProcessor.AccumulatorGenerator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VariantProcessor.Builder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VariantProcessor.ResultMerger.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VcfFileSegment.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VcfFileSegmentGenerator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VcfPathSegment.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/VcfPathSegmentGenerator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/util/PredicateFilterDecoratingClosableIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/util/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/processor/util/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/filter/AlleleBalanceFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/filter/DepthFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/filter/FilterApplyingVariantIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/filter/FilterVcf.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/filter/FisherStrandFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/filter/GenotypeFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/filter/GenotypeQualityFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/filter/QdFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/filter/VariantFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/BafRegressMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/CollectArraysVariantCallingMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/CombineGenotypingArrayVcfs.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/CreateBafRegressMetricsFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/CreateVerifyIDI Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/DistanceMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/ExtractBarcodesProgram.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/ExtractIlluminaBarcodes.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/ExtractIlluminaBarcodes.PerTileBarcodeExtractor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/IlluminaBasecallingMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/IlluminaBasecallsToFastq.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/IlluminaBasecallsToFastq.ReadNameFormat.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/IlluminaBasecallsToSam.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/IlluminaLaneMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/IlluminaPhasingMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/LanePhasingMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/MarkIlluminaAdapters.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/SortedBasecallsConverter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/UnsortedBasecallsConverter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/BaseIlluminaDataProvider.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/BclData.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/CbclData.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/ClusterData.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/IlluminaDataProviderFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/IlluminaDataType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/IlluminaFileUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/IlluminaFileUtil.SupportedIlluminaFormat.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/IlluminaMetricsCode.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/IntensityChannel.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/MultiTileBclFileUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/MultiTileBclParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/MultiTileFileUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/MultiTileFilterParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/MultiTileLocsParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/MultiTileParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/OutputMapping.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/ParameterizedFileUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/PerTileFileUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/PerTileOrPerRunFileUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/PerTileParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/PerTilePerCycleFileUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/PosParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/Range.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/ReadData.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/ReadDescriptor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/ReadStructure.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/ReadStructure.Substructure.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/ReadType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/Tile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/TileIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/TileIndex.TileIndexRecord.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/TileMetr Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/ReadEndsForMateCigar.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/RepresentativeReadIndexerCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/SamRecordWithOrdinalAndSetDuplicateReadFlag.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/Pair.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/PGTagArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/PhysicalLocation.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/PhysicalLocationInt.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/PhysicalLocationShort.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/PrimaryAlignmentKey.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/ReadNameParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/RepresentativeReadIndexer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/SamComparison.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/SamComparison.AlignmentComparison.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/SAMComparisonArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/util/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/BaseCalculator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/BaseErrorAggregation.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/BaseErrorCalculator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/BaseErrorMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/CollectSamErrorMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ErrorMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/IndelErrorCalculator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/IndelErrorMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/OverlappingErrorMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/OverlappingReadsErrorCalculator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.BinnedReadCycleStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.CigarOperatorsInReadStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.CollectionStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.Consensus.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.ConsensusStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.CycleBin.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.FlowCellTileStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.FlowCellXStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.FlowCellYStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.GCContentStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.IndelLengthStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.IndelsInReadStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.LongShortHomopolymer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.LongShortHomopolymerStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.MismatchesInReadStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.NsInReadStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/d Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/MergeableMetricBase.MergeByAdding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/MergeableMetricBase.MergeByAssertEquals.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/MergeableMetricBase.MergingIsManual.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/MergeableMetricBase.NoMergingIsDerived.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/MergeableMetricBase.NoMergingKeepsValue.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/MetricAccumulationLevel.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/QualityScoreDistribution.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/RnaSeqMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/RrbsCpgDetailMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/RrbsMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/RrbsSummaryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/SinglePassSamProgram.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/TheoreticalSensitivity.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/TheoreticalSensitivity.RouletteWheel.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/TheoreticalSensitivityMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/WgsMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/WgsMetricsProcessor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/WgsMetricsProcessorImpl.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/CollectHsMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/CollectTargetedMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/CollectTargetedPcrMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/HsMetricCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/HsMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/InsertSizeMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/PanelMetricsBase.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/RnaSeqMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/RnaSeqMetricsCollector.StrandSpecificity.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/TargetedPcrMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/TargetedPcrMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/TargetMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/TargetMetricsBase.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/TargetMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/TargetMetricsCollector.Coverage.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/TargetMetricsCollector.PerUnitTargetMetricCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/directed/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/replicates/CollectIndependentReplicateMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/replicates/IndependentReplicateMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/replicates/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/replicates/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/CollectSequencingArtifactMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/ConvertSequencingArtifactToOxoG.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/ErrorSummaryMetrics.html using Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/DownsampleSam.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/DuplicationMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/EarliestFragmentPrimaryAlignmentSelectionStrategy.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/FastqToSam.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/FilterSamReads.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/FilterSamReads.Filter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/FixMateInformation.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/GatherBamFiles.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/MergeBamAlignment.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/MergeSamFiles.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/MostDistantPrimaryAlignmentSelectionStrategy.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/PositionBasedDownsampleSam.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/PrimaryAlignmentSelectionStrategy.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/ReorderSam.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/ReplaceSamHeader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/RevertOriginalBaseQualitiesAndAddMateCigar.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/RevertSam.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/RevertSam.FileType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamAlignmentMerger.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamComparisonMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamFormatConverter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamToFastq.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamToFastqWithTags.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SetNmAndUqTags.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SetNmMdAndUqTags.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SortSam.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SplitSamByLibrary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SplitSamByNumberOfReads.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/ValidateSamFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/ValidateSamFile.Mode.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/ViewSam.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/ViewSam.AlignmentStatus.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/ViewSam.PfStatus.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/CheckDuplicateMarking.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/CheckDuplicateMarking.Mode.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/CollectDuplicateMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/EstimateLibraryComplexity.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/MarkDuplicates.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/MarkDuplicates.DuplicateTaggingPolicy.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/MarkDuplicates.DuplicateType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/MarkDuplicatesWithMateCigar.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/MarkDuplicatesWithMateCigarIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/SimpleMarkDuplicatesWithMateCigar.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigar.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/UmiGraph.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-ja Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalList/IntervalListScatterMode.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalList/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalList/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/ClassFinder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/CommandLineDefaults.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/CommandLineProgram.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/CommandLineSyntaxTranslater.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/PicardCommandLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/StandardOptionDefinitions.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/BaseCallingProgramGroup.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/DiagnosticsAndQCProgramGroup.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/GenotypingArraysProgramGroup.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/IntervalsManipulationProgramGroup.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/OtherProgramGroup.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/ReadDataManipulationProgramGroup.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/ReferenceProgramGroup.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/Testing.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/VariantEvaluationProgramGroup.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/VariantFilteringProgramGroup.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/VariantManipulationProgramGroup.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/argumentcollections/EmptyOutputArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/argumentcollections/IntervalArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/argumentcollections/OptionalReferenceArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/argumentcollections/OutputArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/argumentcollections/ReferenceArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/argumentcollections/RequiredOutputArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/argumentcollections/RequiredReferenceArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/argumentcollections/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/argumentcollections/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/VcfToIntervalList.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/VcfToIntervalList.VARIANT_ID_TYPES.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/VcfUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/PairedVariantSubContextIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/PairedVariantSubContextIterator.VcfTuple.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/RenameSampleInVcf.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/SortVcf.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/SplitVcfs.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/UpdateVcfSequenceDictionary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/VcfFormatConverter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/CallingMetricAccumulator.Result.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/CollectVariantCallingMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicar Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/filter/CountingMapQFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/filter/CountingPairedFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/AbstractInputParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/AccumulateQualityYieldMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/AdapterMarker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/AdapterPair.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/AlleleSubsettingUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/AsyncIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/AtomicIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/BaitDesigner.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/BaitDesigner.DesignStrategy.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/BarcodeEditDistanceQuery.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/BasicInputParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/BedToIntervalList.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/CircularByteBuffer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/ClippingUtility.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/CsvInputParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/DbSnpBitSetUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/DbSnpBitSetUtil.DbSnpBitSets.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/DelimitedTextFileWithHeaderIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/DelimitedTextFileWithHeaderIterator.Row.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/FifoBuffer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/GraphUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/GraphUtils.Graph.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IlluminaUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IlluminaUtil.IlluminaAdapterPair.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalListToBed.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalListTools.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalListTools.Action.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/Iterators.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/LiftOverIntervalList.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/LiftoverUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/MathUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/MathUtil.LogMath.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/PropertyUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/QuerySortedReadPairIteratorUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/QuerySortedReadPairIteratorUtil.ReadPair.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/ReflectionUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/RExecutor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/ScatterIntervalsByNs.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/SequenceDictionaryUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/SequenceDictionaryUtils.SamSequenceRecordsIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/SingleBarcodeDistanceMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/TabbedInputParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/TabbedTextFileWithHeaderParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/TabbedTextFileWithHeaderParser.Row.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/ThreadPoolExecutorUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/ThrentensityContaminationMetricsFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/GtcToVcf.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/MergePedIntoVcf.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/VcfToAdpc.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/VerifyIDIntensityContaminationMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/ArraysControlInfo.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/BpmToNormalizationManifestCsv.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/Build37ExtendedIlluminaManifest.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/Build37ExtendedIlluminaManifestRecord.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/Build37ExtendedIlluminaManifestRecord.Flag.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/Build37ExtendedIlluminaManifestRecordCreator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/CompareGtcFiles.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/CreateExtendedIlluminaManifest.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/IlluminaAdpcFileWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/IlluminaAdpcFileWriter.Record.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/IlluminaBPMFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/IlluminaBPMLocusEntry.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/IlluminaGenotype.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/IlluminaManifest.html using File::StripNondeterminism::handlers::javadoc oc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.PairOrientation.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.PairStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.ProperPaired.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.ReadDirection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.ReadOrdinality.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/ReadBaseStratification.RecordAndOffsetStratifier.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/SimpleErrorCalculator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/SamErrorMetric/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/resources/glass.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/resources/x.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/images/ui-bg_glass_65_dadada_1x400.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/images/ui-icons_454545_256x240.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/images/ui-bg_glass_95_fef1ec_1x400.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/images/ui-bg_glass_75_dadada_1x400.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/images/ui-bg_highlight-soft_75_cccccc_1x100.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/images/ui-icons_888888_256x240.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/images/ui-icons_2e83ff_256x240.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/images/ui-icons_cd0a0a_256x240.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/images/ui-bg_glass_55_fbf9ee_1x400.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/images/ui-icons_222222_256x240.png using File::StripNondeterminism::handlers::png Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/images/ui-bg_glass_75_e6e6e6_1x400.png using File::StripNondeterminism::handlers::png icsUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/TilePhasingValue.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/TileTemplateRead.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/BarcodeFileFaker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/BciFileFaker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/BclFileFaker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/BclIndexFaker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/ClocsFileFaker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/FileFaker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/FilterFileFaker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/LocsFileFaker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/MultiTileBclFileFaker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/MultiTileLocsFileFaker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/PosFileFaker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/fakers/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/parser/readers/package-tree.html using File::StripNondeterminism::handlers::javadoc terminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fastq/BamToBfqWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fastq/Casava18ReadNameEncoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fastq/IlluminaReadNameEncoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fastq/ReadNameEncoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fastq/SamToBfqWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fastq/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/annotation/AnnotationException.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/annotation/Gene.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/annotation/Gene.Transcript.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/annotation/Gene.Transcript.Exon.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/annotation/GeneAnnotationReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/annotation/LocusFunction.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/annotation/RefFlatReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/annotation/RefFlatReader.RefFlatColumns.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/annotation/SortGff.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/annotation/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/annotation/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/filter/CountingAdapterFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/filter/CountingDuplicateFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/filter/CountingFilter.html using File::StripNondeterminism::handlers::javadoc d-java/api/picard/vcf/CollectVariantCallingMetrics.VariantCallingDetailMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/CollectVariantCallingMetrics.VariantCallingSummaryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/FixVcfHeader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GA4GHScheme.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GA4GHSchemeWithMissingAsHomRef.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GatherVcfs.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordance.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordance.Alleles.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceContingencyMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceCounts.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceDetailMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceScheme.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceSchemeFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceStateCodes.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceStates.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceStates.CallState.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceStates.ContingencyState.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceStates.TruthAndCallStates.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceStates.TruthState.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GenotypeConcordanceSummaryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/vcf/GvcfMetricAccumulator.html using File::StripNondeterminism::handlers::javadoc adPoolExecutorWithExceptions.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/UnsignedTypeUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/VariantType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/help/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/help/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/help/HelpConstants.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/help/PicardHelpDoclet.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/help/PicardHelpDocWorkUnitHandler.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalList/IntervalListScatter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalList/IntervalListScatterer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalList/IntervalListScattererByBaseCount.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalList/IntervalListScattererByIntervalCount.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalList/IntervalListScattererByIntervalCountWithDistributedRemainder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalList/IntervalListScattererWithoutSubdivision.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalList/IntervalListScattererWithoutSubdivisionWithOverflow.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/util/IntervalList/IntervalListScattererWithSubdivision.html using File::StripNondeterminism::handlers::javadoc va/api/picard/sam/markduplicates/UmiMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/AbstractOpticalDuplicateFinderCommandLineProgram.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/DiskBasedReadEndsForMarkDuplicatesMap.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/LibraryIdGenerator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/MarkQueue.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/MemoryBasedReadEndsForMarkDuplicatesMap.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/OpticalDuplicateFinder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/PhysicalLocationForMateCigar.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/PhysicalLocationForMateCigarSet.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/ReadEnds.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/ReadEndsForMarkDuplicates.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesMap.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesWithBarcodes.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesWithBarcodesCodec.html using File::StripNondeterminism::handlers::javadoc File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/SequencingArtifactMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/SequencingArtifactMetrics.BaitBiasDetailMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/SequencingArtifactMetrics.BaitBiasSummaryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/SequencingArtifactMetrics.PreAdapterDetailMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/SequencingArtifactMetrics.PreAdapterSummaryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/Transition.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/Transition.Base.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/artifacts/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/BarcodeExtractor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/BarcodeExtractor.BarcodeMatch.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/BarcodeMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/BasecallsConverter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/BasecallsConverter.ClusterDataConverter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/BasecallsConverter.ConvertedClusterDataWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/BasecallsConverterBuilder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/CheckIlluminaDirectory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/ClusterDataToSamConverter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/CollectIlluminaBasecallingMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/CollectIlluminaLaneMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/illumina/CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/IlluminaManifestRecord.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/IlluminaManifestRecord.IlluminaStrand.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/InfiniumDataFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/InfiniumEGTFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/InfiniumFileTOC.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/InfiniumGTCFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/InfiniumGTCRecord.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/InfiniumNormalizationManifest.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/InfiniumTransformation.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/InfiniumVcfFields.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/InfiniumVcfFields.GENOTYPE_VALUES.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/CalculateFingerprintMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/CappedHaplotypeProbabilities.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/CheckFingerprint.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/ClusterCrosscheckMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/ClusteredCrosscheckMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/ConvertHaplotypeDatabaseToVcf.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/CrosscheckFingerprints.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/CrosscheckMetric.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/CrosscheckMetric.DataType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/CrosscheckMetric.FingerprintResult.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/CrosscheckReadGroupFingerprints.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/DiploidGenotype.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/DiploidHaplotype.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/ExtractFingerprint.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/Fingerprint.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/FingerprintChecker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/FingerprintIdDetails.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/FingerprintMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/FingerprintResults.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/FingerprintUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/FingerprintUtils.VariantContextSet.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/HaplotypeBlock.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/HaplotypeMap.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/HaplotypeProbabilities.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/HaplotypeProbabilities.Genotype.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/HaplotypeProbabilitiesFromContaminatorSequence.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/HaplotypeProbabilitiesFromGenotype.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/HaplotypeProbabilitiesFromGenotypeLikelihoods.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/HaplotypeProbabilitiesFromSequence.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/HaplotypeProbabilityOfNormalGivenTumor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/IdentifyContaminant.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/LiftOverHaplotypeMap.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/MatchResults.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/Snp.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/package-summary.html using File::Stri Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/constant-values.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/serialized-form.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/overview-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/package-search-index.zip using File::StripNondeterminism::handlers::zip Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/type-search-index.zip using File::StripNondeterminism::handlers::zip Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/member-search-index.zip using File::StripNondeterminism::handlers::zip Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/index-all.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/allclasses-index.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/allpackages-index.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/deprecated-list.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/allclasses.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/index.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/overview-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/help-doc.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/PicardException.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/Test.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/AbstractWgsMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/AdapterUtility.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/AlignmentSummaryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/AlignmentSummaryMetrics.Category.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/AlignmentSummaryMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/BaseDistributionByCycleMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/ChimeraUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectAlignmentSummaryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectBaseDistributionByCycle.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectGcBiasMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectInsertSizeMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectJumpingLibraryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectMultipleMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectMultipleMetrics.Program.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectMultipleMetrics.ProgramInterface.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectOxoGMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectOxoGMetrics.CpcgMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectQualityYieldMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectQualityYieldMetrics.QualityYieldMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectQualityYieldMetrics.QualityYieldMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectRawWgsMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectRawWgsMetrics.RawWgsMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectRnaSeqMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectRrbsMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectWgsMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectWgsMetrics.WgsMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicardpNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/fingerprint/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/reference/ExtractSequences.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/reference/NonNFastaSize.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/reference/NormalizeFasta.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/reference/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/reference/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/AbstractAlignmentMerger.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/AbstractAlignmentMerger.UnmappingReadStrategy.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/AddCommentsToBam.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/AddOATag.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/AddOrReplaceReadGroups.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/BamIndexStats.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/BestEndMapqPrimaryAlignmentStrategy.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/BestMapqPrimaryAlignmentSelectionStrategy.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/BuildBamIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/CalculateReadGroupChecksum.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/CheckTerminatorBlock.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/CleanSam.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/CompareSAMs.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/sam/CreateSequenceDictionary.html using File::StripNondeterminism::handlers::javadoc -java/api/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CompareMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CounterManager.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/CounterManager.Counter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/FastWgsMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/FingerprintingDetailMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/FingerprintingSummaryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/GcBiasDetailMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/GcBiasMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/GcBiasSummaryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/GcBiasUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/InsertSizeMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/JumpingLibraryMetrics.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/MeanQualityByCycle.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/analysis/MergeableMetricBase.html using File::StripNondeterminism::handlers::javadoc dh_compress -i -O--buildsystem=gradle cd debian/picard-tools cd debian/libpicard-java cd debian/libpicard-java-doc chmod a-x usr/share/doc/libpicard-java/changelog.Debian chmod a-x usr/share/doc/picard-tools/changelog.Debian usr/share/doc/picard-tools/mini.vcf usr/share/man/man1/PicardCommandLine.1 gzip -9nf usr/share/doc/libpicard-java/changelog.Debian gzip -9nf usr/share/doc/picard-tools/changelog.Debian usr/share/doc/picard-tools/mini.vcf usr/share/man/man1/PicardCommandLine.1 chmod a-x usr/share/doc/libpicard-java-doc/changelog.Debian gzip -9nf usr/share/doc/libpicard-java-doc/changelog.Debian cd '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg' cd '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg' cd '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg' rm -f debian/picard-tools/usr/share/man/man1/picard-tools.1 debian/picard-tools/usr/share/man/man1/picard-tools.1.gz ln -s PicardCommandLine.1.gz debian/picard-tools/usr/share/man/man1/picard-tools.1.gz dh_fixperms -i -O--buildsystem=gradle find debian/picard-tools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libpicard-java ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libpicard-java-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libpicard-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libpicard-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/picard-tools/usr/share/doc -type f -a -true -a ! -regex 'debian/picard-tools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libpicard-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/picard-tools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libpicard-java-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libpicard-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/picard-tools/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libpicard-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/picard-tools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/picard-tools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/libpicard-java-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libpicard-java-doc/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libpicard-java-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -i -O--buildsystem=gradle dh_installdeb -i -O--buildsystem=gradle install -d debian/picard-tools/DEBIAN install -d debian/libpicard-java/DEBIAN install -d debian/libpicard-java-doc/DEBIAN rm -f debian/libpicard-java-doc.debhelper.log debian/libpicard-java.debhelper.log debian/picard-tools.debhelper.log debian/rules override_dh_gencontrol make[1]: Entering directory '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg' cat debian/control \ | sed -e '/^Build-.*Depends:/,/^[^[:space:]#]/{s/^Build-.*Depends:/ /;p};d' \ | grep '^[[:space:]]' \ | tr ',' '\n' \ > debian/bd-temp-substvars echo -n "bd:libhtsjdk-java=" > debian/bd.substvars grep 'libhtsjdk-java ' debian/bd-temp-substvars \ | tr "\n" "," \ | sed -e 's/[[:space:]]\+/ /g;s/,$/\n/' \ >> debian/bd.substvars echo -n "bd:libguava-java=" >> debian/bd.substvars grep 'libguava-java ' debian/bd-temp-substvars \ | tr "\n" "," \ | sed -e 's/[[:space:]]\+/ /g;s/,$/\n/' \ >> debian/bd.substvars dh_gencontrol -O--buildsystem=gradle -- -Tdebian/bd.substvars echo misc:Depends= >> debian/picard-tools.substvars echo misc:Pre-Depends= >> debian/picard-tools.substvars dpkg-gencontrol -ppicard-tools -ldebian/changelog -Tdebian/picard-tools.substvars -Pdebian/picard-tools -Tdebian/bd.substvars echo misc:Depends= >> debian/libpicard-java.substvars echo misc:Pre-Depends= >> debian/libpicard-java.substvars dpkg-gencontrol -plibpicard-java -ldebian/changelog -Tdebian/libpicard-java.substvars -Pdebian/libpicard-java -Tdebian/bd.substvars echo misc:Depends= >> debian/libpicard-java-doc.substvars echo misc:Pre-Depends= >> debian/libpicard-java-doc.substvars dpkg-gencontrol -plibpicard-java-doc -ldebian/changelog -Tdebian/libpicard-java-doc.substvars -Pdebian/libpicard-java-doc -Tdebian/bd.substvars dpkg-gencontrol: warning: package libpicard-java: substitution variable ${java:Depends} unused, but is defined chmod 0644 -- debian/libpicard-java/DEBIAN/control dpkg-gencontrol: warning: package picard-tools: substitution variable ${bd:libhtsjdk-java} unused, but is defined chmod 0644 -- debian/picard-tools/DEBIAN/control dpkg-gencontrol: warning: package libpicard-java-doc: substitution variable ${bd:libhtsjdk-java} unused, but is defined chmod 0644 -- debian/libpicard-java-doc/DEBIAN/control make[1]: Leaving directory '/build/picard-tools-BIO3c2/picard-tools-2.27.1+dfsg' dh_md5sums -i -O--buildsystem=gradle cd debian/picard-tools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libpicard-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libpicard-java-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/picard-tools/DEBIAN/md5sums chmod 0644 -- debian/libpicard-java/DEBIAN/md5sums chmod 0644 -- debian/libpicard-java-doc/DEBIAN/md5sums dh_builddeb -i -O--buildsystem=gradle dpkg-deb --root-owner-group --build debian/picard-tools .. dpkg-deb --root-owner-group --build debian/libpicard-java .. dpkg-deb --root-owner-group --build debian/libpicard-java-doc .. dpkg-deb: building package 'picard-tools' in '../picard-tools_2.27.1+dfsg-1_all.deb'. dpkg-deb: building package 'libpicard-java' in '../libpicard-java_2.27.1+dfsg-1_all.deb'. dpkg-deb: building package 'libpicard-java-doc' in '../libpicard-java-doc_2.27.1+dfsg-1_all.deb'. dpkg-genbuildinfo --build=all -O../picard-tools_2.27.1+dfsg-1_all.buildinfo dpkg-genchanges --build=all -O../picard-tools_2.27.1+dfsg-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/picard-tools-BIO3c2 /tmp/picard-tools-2.27.1+dfsg-1e418iazm I: cleaning package lists and apt cache... W: deleting files in /tmp: hsperfdata_root W: deleting files in /tmp: hsperfdata_builduser I: removing tempdir /tmp/mmdebstrap.FC3tULMeW0... I: success in 1074.2903 seconds md5: libpicard-java-doc_2.27.1+dfsg-1_all.deb: OK md5: libpicard-java_2.27.1+dfsg-1_all.deb: OK md5: picard-tools_2.27.1+dfsg-1_all.deb: OK sha1: libpicard-java-doc_2.27.1+dfsg-1_all.deb: OK sha1: libpicard-java_2.27.1+dfsg-1_all.deb: OK sha1: picard-tools_2.27.1+dfsg-1_all.deb: OK sha256: libpicard-java-doc_2.27.1+dfsg-1_all.deb: OK sha256: libpicard-java_2.27.1+dfsg-1_all.deb: OK sha256: picard-tools_2.27.1+dfsg-1_all.deb: OK Checksums: OK