debian/0000755000000000000000000000000012256262374007177 5ustar debian/source/0000755000000000000000000000000012231421547010467 5ustar debian/source/format0000644000000000000000000000001412231421547011675 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000001370212256261751011133 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://picard.svn.sourceforge.net/viewvc/picard/tags/1.101/ Comment: Some source files are removed, see debian/rules. Files: * Copyright: © 2009–2011 The Broad Institute License: MIT Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Files: src/java/net/sf/samtools/util/DateParser.java Copyright: 2000 MIT, INRIA and Keio License: W3C-Software W3C IPR SOFTWARE NOTICE . Copyright 1995-1998 World Wide Web Consortium, (Massachusetts Institute of Technology, Institut National de Recherche en Informatique et en Automatique, Keio University). All Rights Reserved. http://www.w3.org/Consortium/Legal/ . 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Files: src/java/net/sf/samtools/util/SeekableStream.java Copyright: 2007-2009 the Broad Institute/Massachusetts Institute of Technology License: GPL-2 This is copyright (2007-2009) by the Broad Institute/Massachusetts Institute of Technology. It is licensed to You under the GNU General Public License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . http://www.opensource.org/licenses/gpl-2.0.php . This software is supplied without any warranty or guaranteed support whatsoever. Neither the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. Comment: On Debian systems, the complete text of the GNU General Public License version 2 is available in the file ‘/usr/share/common-licenses/GPL-2’. Files: etc/test/junit-noframes.xsl Copyright: 2001-2004 The Apache Software Foundation License: Apache-2.0 Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . http://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. Comment: On Debian systems, the complete text of the Apache License version 2.0 is available in the file ‘/usr/share/common-licenses/Apache-2.0’. Files: debian/* Copyright: 2010 Shaun Jackman 2013 Olivier Sallou License: ISC Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. debian/libsam-java.install0000644000000000000000000000003612231421547012744 0ustar dist/sam-*.jar usr/share/java debian/gbp.conf0000644000000000000000000000016512231421547010610 0ustar # This package is managed with git-buildpackage and pristine-tar. [DEFAULT] # use pristine-tar: pristine-tar = True debian/compat0000644000000000000000000000000212231421547010365 0ustar 9 debian/picard-tools.10000644000000000000000000000243412231421547011654 0ustar .TH picard-tools "1" "July 2013" "picard-tools 1.95" "User Commands" .SH NAME picard-tools \- manipulate SAM and BAM files .SH SYNOPSIS \fBpicard-tools\fR \fICOMMAND\fR [\fIOPTION\fR]... .SH DESCRIPTION SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Picard Tools includes these utilities to manipulate SAM and BAM files: AddOrReplaceReadGroups BamToBfq BamIndexStats BuildBamIndex CalculateHsMetrics CleanSam CollectAlignmentSummaryMetrics CollectGcBiasMetrics CollectInsertSizeMetrics CollectMultipleMetrics CollectTargetedPcrMetrics CollectRnaSeqMetrics CompareSAMs CreateSequenceDictionary DownsampleSam ExtractIlluminaBarcodes EstimateLibraryComplexity FastqToSam FilterSamReads FixMateInformation IlluminaBasecallsToFastq IlluminaBasecallsToSam CheckIlluminaDirectory IntervalListTools MarkDuplicates MeanQualityByCycle MergeBamAlignment MergeSamFiles MergeVcfs NormalizeFasta ExtractSequences QualityScoreDistribution ReorderSam ReplaceSamHeader RevertSam SamFormatConverter SamToFastq SortSam VcfFormatConverter SplitVcfs ValidateSamFile ViewSam .SH "REPORTING BUGS" samtools-devel@lists.sourceforge.net .SH COPYRIGHT Copyright 2010 The Broad Institute .SH "SEE ALSO" http://picard.sourceforge.net/ debian/README.source0000644000000000000000000000030512231421547011344 0ustar The original source was packaged from the upstream subversion repository: debian/rules get-orig-source Binary files in lib/* have been removed. -- Shaun Jackman 2010-06-15 debian/watch0000644000000000000000000000005512231421547010220 0ustar version=3 http://sf.net/picard/sam-(.+)\.jar debian/picard-tools.install0000644000000000000000000000017112231421547013156 0ustar debian/bin/picard-tools usr/bin dist/picard-*.jar usr/share/java src/scripts/explain_sam_flags.py usr/share/picard-tools debian/picard-tools.README.Debian0000644000000000000000000000052712231421547013633 0ustar The Python script ‘explain_sam_flags.py’ is distributed in ‘/usr/share/picard-tools/’ as a convenience for the users, but the package does not depend on it. You can install the default Python version in Debian with the following command: apt-get install python -- Charles Plessy Tue, 06 Jul 2010 16:29:56 +0900 debian/picard-tools.manpages0000644000000000000000000000002612231421547013302 0ustar debian/picard-tools.1 debian/patches/0000755000000000000000000000000012256260705010622 5ustar debian/patches/use_libjbzip2-java0000644000000000000000000000407712256260705014237 0ustar Subject: use libjbzip2-java classes Description: Debian package for this class is libjbzip2-java, need to update package name Author: Olivier Sallou Last-Updated: 2012-08-31 Forwarded: not-needed --- a/src/java/net/sf/picard/io/IoUtil.java +++ b/src/java/net/sf/picard/io/IoUtil.java @@ -35,8 +35,8 @@ import java.util.zip.GZIPInputStream; import java.util.zip.GZIPOutputStream; -import org.apache.tools.bzip2.CBZip2InputStream; -import org.apache.tools.bzip2.CBZip2OutputStream; +import org.itadaki.bzip2.BZip2InputStream; +import org.itadaki.bzip2.BZip2OutputStream; /** * A class for utility methods that wrap or aggregate functionality in Java IO. @@ -232,12 +232,12 @@ try { final FileInputStream fis = new FileInputStream(file); - if(fis.read() != 66 || fis.read() != 90) { //Read magic number 'BZ' or else CBZip2InputStream will complain about it + if(fis.read() != 66 || fis.read() != 90) { //Read magic number 'BZ' or else BZip2InputStream will complain about it fis.close(); throw new PicardException(file.getAbsolutePath() + " is not a BZIP file."); } - return new CBZip2InputStream(fis); + return new BZip2InputStream(fis, false); } catch (IOException ioe) { throw new PicardException("Error opening file: " + file.getName(), ioe); @@ -344,9 +344,9 @@ try { final FileOutputStream fos = new FileOutputStream(file, append); - fos.write(66); //write magic number 'BZ' because CBZip2OutputStream does not do it for you + fos.write(66); //write magic number 'BZ' because BZip2OutputStream does not do it for you fos.write(90); - return new BufferedOutputStream(new CBZip2OutputStream(fos), Defaults.BUFFER_SIZE); + return new BufferedOutputStream(new BZip2OutputStream(fos), Defaults.BUFFER_SIZE); } catch (IOException ioe) { throw new PicardException("Error opening file for writing: " + file.getName(), ioe); debian/patches/01-build.xml0000644000000000000000000000467012231422606012661 0ustar Description: Modifies the upstream build system. This patch changes the path to the javac compiler, enables the use of the system's testng library, and adds a new target for preparing the sam and picard jar files and installing the extra R scripts from src/scripts/net/sf/picard/analysis/. Origin: vendor Forwarded: no --- a/build.xml +++ b/build.xml @@ -23,7 +23,7 @@ ~ THE SOFTWARE. --> - + @@ -53,7 +53,7 @@ - + @@ -72,6 +72,11 @@ + + + + + @@ -205,8 +210,9 @@ + + - @@ -236,6 +242,8 @@ + + Uploaders: Shaun Jackman , Charles Plessy , Olivier Sallou Build-Depends: ant, default-jdk, testng, libsnappy1.0.3-java, debhelper (>= 9), libjbzip2-java, libcofoja-java, libcommons-jexl2-java, javahelper (>=0.25), python Standards-Version: 3.9.5 Homepage: http://picard.sourceforge.net/ Vcs-Git: git://anonscm.debian.org/debian-med/picard-tools.git Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/picard-tools.git Package: libsam-java Section: java Architecture: all Depends: ${misc:Depends} Suggests: picard-tools Description: Java library to manipulate SAM and BAM files SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Package: picard-tools Architecture: all Depends: default-jre | java6-runtime, ${misc:Depends}, libsam-java (>= ${source:Version}), ${python:Depends}, libjbzip2-java, libcofoja-java, libcommons-jexl2-java Suggests: python, r-base-core Description: Command line tools to manipulate SAM and BAM files SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Picard Tools includes these utilities to manipulate SAM and BAM files: BamToBfq IlluminaBasecallsToSam BuildBamIndex MarkDuplicates CalculateHsMetrics MeanQualityByCycle CleanSam MergeBamAlignment CollectAlignmentSummaryMetrics MergeSamFiles CollectGcBiasMetrics NormalizeFasta CollectInsertSizeMetrics QualityScoreDistribution CollectRnaSeqMetrics ReplaceSamHeader CompareSAMs RevertSam CreateSequenceDictionary SamFormatConverter ExtractIlluminaBarcodes SamToFastq EstimateLibraryComplexity SortSam FastqToSam ValidateSamFile FixMateInformation ViewSam debian/bin/0000755000000000000000000000000012231421547007737 5ustar debian/bin/picard-tools0000755000000000000000000000761712231421547012300 0ustar #!/bin/sh set -eu if [ `basename -- $0` = picard-tools ]; then if [ $# = 0 ]; then cat 1>&2 <&2 picard-tools: unrecognized command "'$command'"; exit 1 esac p=/usr/share/java exec java ${JAVA_OPTIONS-} -XX:MaxPermSize=256m -cp $p/jbzip2.jar:$p/picard.jar:$p/sam.jar:$p/cofoja.jar:$p/commons-jexl2.jar $main "$@" debian/rules0000755000000000000000000000252712231422606010252 0ustar #!/usr/bin/make -f export DH_OPTIONS export ANT_HOME=/usr/share/ant export JAVA_HOME=$(readlink -f /usr/bin/javac | sed "s:/bin/javac::") %: dh $@ --with javahelper,python2 override_dh_auto_build: dh_auto_build -- -Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5 override_dh_auto_configure: [ -d lib ] || mkdir lib # This empty directory is lost in the packages's Git clone. dh_auto_configure # Adapted from http://wiki.debian.org/SandroTosi/Svn_get-orig-source PACKAGE = picard-tools SRC_VERSION = $(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') SRC_DIR = $(PACKAGE)-$(SRC_VERSION).orig TARBALL = $(PACKAGE)_$(SRC_VERSION).orig.tar.xz SVN_REPOS= http://svn.code.sf.net/p/picard/code .PHONY: get-orig-source get-orig-source: rm -rf get-orig-source $(TARBALL) mkdir get-orig-source svn export $(SVN_REVISION) $(SVN_REPOS)/tags/$(SRC_VERSION) get-orig-source/$(SRC_DIR) # Removing convenience binary jar files. rm -r get-orig-source/$(SRC_DIR)/lib/* tar cJf $(TARBALL) -C get-orig-source $(SRC_DIR) rm -r get-orig-source @echo " "$(TARBALL)" created; move it to the right destination to build the package" override_dh_link: dh_link -p libsam-java usr/share/java/sam-$(SRC_VERSION).jar usr/share/java/sam.jar dh_link -p picard-tools usr/share/java/picard-$(SRC_VERSION).jar usr/share/java/picard.jar debian/picard-tools.classpath0000644000000000000000000000021212231421547013466 0ustar usr/share/java/picard.jar /usr/share/java/commons-jexl2.jar /usr/share/java/cofoja.jar /usr/share/java/jbzip2.jar /usr/share/java/sam.jar debian/changelog0000644000000000000000000001042412256262023011041 0ustar picard-tools (1.105-1) unstable; urgency=low * New upstream release 1.105 * Conforms with Policy 3.9.5. -- Olivier Sallou Tue, 24 Dec 2013 11:16:18 +0100 picard-tools (1.100-1) unstable; urgency=low [Charles Plessy] * Imported Upstream version 1.100 * Compress the source archive with XZ. * Mark the use of git-buildpackage and pristine-tar with a gbp.conf file. [Olivier Sallou] * d/rules: fix build for release -- Charles Plessy Sun, 20 Oct 2013 10:38:11 +0900 picard-tools (1.95-1) unstable; urgency=low * New upstream release * Fix man page with missing tools from previous releases * Fix picard-tools binary to manage missing tools from previous releases * Fix management of JAVA_OPTIONS if not set at all. -- Olivier Sallou Thu, 25 Jul 2013 13:36:02 +0200 picard-tools (1.90-3) unstable; urgency=low * Add possibility to specify JAVA options (Closes: #705681), with JAVA_OPTIONS env variable. -- Olivier Sallou Tue, 09 Jul 2013 09:20:07 +0200 picard-tools (1.90-2) unstable; urgency=low * Load in unstable, all deps are available. -- Olivier Sallou Sun, 02 Jun 2013 10:57:05 +0200 picard-tools (1.90-1) experimental; urgency=low * New upstream release -- Olivier Sallou Wed, 01 May 2013 13:57:05 +0200 picard-tools (1.87-1) experimental; urgency=low * New upstream release -- Olivier Sallou Wed, 01 May 2013 15:14:04 +0100 picard-tools (1.82-2) unstable; urgency=low * Fix classpath for BuildBamIndex (Closes: #705686). -- Olivier Sallou Fri, 19 Apr 2013 14:26:23 +0200 picard-tools (1.82-1) unstable; urgency=low * New upstream release -- Olivier Sallou Thu, 03 Jan 2013 10:46:26 +0100 picard-tools (1.80-1) unstable; urgency=low * New upstream release -- Olivier Sallou Sun, 02 Dec 2012 23:10:10 +0100 picard-tools (1.79-1) unstable; urgency=low * New upstream release 1.79 -- Olivier Sallou Mon, 29 Oct 2012 08:58:44 +0100 picard-tools (1.78-1) unstable; urgency=low * New upstream release -- Olivier Sallou Sat, 13 Oct 2012 11:20:49 +0200 picard-tools (1.77-1) unstable; urgency=low * New upstream release -- Olivier Sallou Fri, 21 Sep 2012 16:41:23 +0200 picard-tools (1.76-1) unstable; urgency=low * New upstream release -- Olivier Sallou Fri, 07 Sep 2012 11:44:03 +0200 picard-tools (1.75-1) unstable; urgency=low [Olivier Sallou] * New upstream releases. * Build-depend on libsnappy1.0.3-java (debian/control). [Charles Plessy] * Refreshed debian/patches/01-build.xml. * Use default java implementation. - debian/control: BD on default-jdk, switch runtime dependency to default-jre | java6-runtime. - debian/rules: Specify source/target = 1.5 to ensure that backwards compatible bytecode is built. - Closes: #684172, thanks to J. Page and Ubuntu. -- Olivier Sallou Thu, 06 Sep 2012 09:10:11 +0900 picard-tools (1.46-1) unstable; urgency=low * New upstream release. * Depend on ${python:Depends} (debian/changelog). * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/changelog, no changes needed). * Corrected and validated debian/copyright machine-readable format. -- Charles Plessy Fri, 03 Jun 2011 20:50:00 +0900 picard-tools (1.41-1) unstable; urgency=low * New upstream release. Closes: #619201. * Add five commands to bin/picard-tools and picard-tools.1. -- Shaun Jackman Tue, 22 Mar 2011 10:52:23 -0700 picard-tools (1.27-1) unstable; urgency=low * New upstream release. * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/changelog, no changes needed). -- Charles Plessy Tue, 03 Aug 2010 20:20:10 +0900 picard-tools (1.25-1) unstable; urgency=low * New upstream release. -- Shaun Jackman Tue, 06 Jul 2010 16:06:18 -0700 picard-tools (1.24-1) UNRELEASED; urgency=low * Initial release. Closes: #586015. -- Shaun Jackman Tue, 15 Jun 2010 10:41:09 -0700