This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository varscan.
commit c8838c6ed063f6c6c6abfb564816abf08da43646 Author: Andreas Tille <[email protected]> Date: Wed Jul 8 05:17:17 2015 +0200 cme fix dpkg-control; update changelog; really drop unused quilt patch --- debian/changelog | 2 + debian/control | 11 ++-- debian/patches/series | 1 - debian/patches/usage.patch | 159 --------------------------------------------- 4 files changed, 8 insertions(+), 165 deletions(-) diff --git a/debian/changelog b/debian/changelog index 2db5e96..725c547 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,6 +1,8 @@ varscan (2.3.9+dfsg-1) UNRELEASED; urgency=medium * New upstream version + * Do not use patches to fix usage any more but fix it using sed in debian/rules + * cme fix dpkg-control -- Andreas Tille <[email protected]> Wed, 08 Jul 2015 04:54:26 +0200 diff --git a/debian/control b/debian/control index 9d0427e..71ec949 100644 --- a/debian/control +++ b/debian/control @@ -1,14 +1,15 @@ Source: varscan -Section: non-free/science -Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Andreas Tille <[email protected]> +Section: non-free/science +XS-Autobuild: no +Priority: optional Build-Depends: debhelper (>= 9), - javahelper (>=0.25), + javahelper, default-jdk, ant -Standards-Version: 3.9.5 -Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/varscan.git +Standards-Version: 3.9.6 +Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/varscan.git Vcs-Git: git://anonscm.debian.org/debian-med/varscan.git Homepage: http://varscan.sourceforge.net/ diff --git a/debian/patches/series b/debian/patches/series deleted file mode 100644 index 3060795..0000000 --- a/debian/patches/series +++ /dev/null @@ -1 +0,0 @@ -# usage.patch diff --git a/debian/patches/usage.patch b/debian/patches/usage.patch deleted file mode 100644 index 1777246..0000000 --- a/debian/patches/usage.patch +++ /dev/null @@ -1,159 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Updated: Tue, 15 Apr 2014 13:38:37 +0200 -Forwarded: no -Description: Adapt usage message to Debian installation - ---- a/net/sf/varscan/CallMpileup.java -+++ b/net/sf/varscan/CallMpileup.java -@@ -28,7 +28,7 @@ public class CallMpileup { - public CallMpileup(String[] args, String callType) - { - // Define the usage message // -- String usage = "USAGE: java -jar VarScan.jar mpileup2cns [pileup file] OPTIONS\n" + -+ String usage = "USAGE: varscan mpileup2cns [pileup file] OPTIONS\n" + - "\tmpileup file - The SAMtools mpileup file\n" + - "\n" + - "\tOPTIONS:\n" + ---- a/net/sf/varscan/CallPileup.java -+++ b/net/sf/varscan/CallPileup.java -@@ -24,7 +24,7 @@ public class CallPileup { - public CallPileup(String[] args, String callType) - { - // Define the usage message // -- String usage = "USAGE: java -jar VarScan.jar pileup2cns [pileup file] OPTIONS\n" + -+ String usage = "USAGE: varscan pileup2cns [pileup file] OPTIONS\n" + - "\tpileup file - The SAMtools pileup file\n" + - "\n" + - "\tOPTIONS:\n" + ---- a/net/sf/varscan/Comparison.java -+++ b/net/sf/varscan/Comparison.java -@@ -27,7 +27,7 @@ public class Comparison { - - public Comparison(String[] args) - { -- String usage = "USAGE: java -jar VarScan.jar compare [file1] [file2] [type] [output] OPTIONS\n" + -+ String usage = "USAGE: varscan compare [file1] [file2] [type] [output] OPTIONS\n" + - "\tfile1 - A file of chromosome-positions, tab-delimited\n" + - "\tfile2 - A file of chromosome-positions, tab-delimited\n" + - "\ttype - Type of comparison [intersect|merge|unique1|unique2]\n" + ---- a/net/sf/varscan/CopyCaller.java -+++ b/net/sf/varscan/CopyCaller.java -@@ -28,7 +28,7 @@ import java.util.HashMap; - public class CopyCaller { - public CopyCaller(String[] args, HashMap<String, String> params) - { -- String usage = "USAGE: java -jar VarScan.jar copyCaller [varScan.copynumber] OPTIONS\n" + -+ String usage = "USAGE: varscan copyCaller [varScan.copynumber] OPTIONS\n" + - "This command will adjust VarScan copynumber output for GC content, apply amp/del thresholds,\n and (optionally) recenter the data\n" + - "\tINPUT:\n" + - "\tRaw output from the VarScan copynumber command (eg. varScan.output.copynumber)\n\n" + ---- a/net/sf/varscan/Copynumber.java -+++ b/net/sf/varscan/Copynumber.java -@@ -22,7 +22,7 @@ public class Copynumber { - //////////////////////////////////////////////////////////////////////////////////////////////////// - public Copynumber(String[] args, boolean isMpileup) - { -- String usage = "USAGE: java -jar VarScan.jar copynumber [normal-tumor.mpileup] [Opt: output] OPTIONS\n" + -+ String usage = "USAGE: varscan copynumber [normal-tumor.mpileup] [Opt: output] OPTIONS\n" + - "\tnormal-tumor.mpileup - The SAMtools mpileup file for Normal and Tumor\n" + - "\toutput - Output base name for files\n" + - "\nOPTIONS:\n" + ---- a/net/sf/varscan/Coverage.java -+++ b/net/sf/varscan/Coverage.java -@@ -29,7 +29,7 @@ public class Coverage { - public Coverage(String[] args) - { - // Define the usage message // -- String usage = "USAGE: java -jar VarScan.jar coverage [pileup-file] OPTIONS\n" + -+ String usage = "USAGE: varscan coverage [pileup-file] OPTIONS\n" + - "\n" + - "\tpileup-file - A SAMtools pileup file or piped input\n" + - "\tOPTIONS:\n" + ---- a/net/sf/varscan/FilterSomatic.java -+++ b/net/sf/varscan/FilterSomatic.java -@@ -29,7 +29,7 @@ public class FilterSomatic { - public FilterSomatic(String[] args) - { - // Define the usage message // -- String usage = "USAGE: java -jar VarScan.jar filter [variant file] OPTIONS\n" + -+ String usage = "USAGE: varscan filter [variant file] OPTIONS\n" + - "\tvariant file - A file of SNPs or indels\n" + - "\n" + - "\tOPTIONS:\n" + ---- a/net/sf/varscan/FilterVariants.java -+++ b/net/sf/varscan/FilterVariants.java -@@ -28,7 +28,7 @@ public class FilterVariants { - public FilterVariants(String[] args) - { - // Define the usage message // -- String usage = "USAGE: java -jar VarScan.jar filter [variant file] OPTIONS\n" + -+ String usage = "USAGE: varscan filter [variant file] OPTIONS\n" + - "\tvariant file - A file of SNPs or indels\n" + - "\n" + - "\tOPTIONS:\n" + ---- a/net/sf/varscan/LimitVariants.java -+++ b/net/sf/varscan/LimitVariants.java -@@ -27,7 +27,7 @@ public class LimitVariants { - - public LimitVariants(String[] args) - { -- String usage = "USAGE: java -jar VarScan.jar limit [infile] OPTIONS\n" + -+ String usage = "USAGE: varscan limit [infile] OPTIONS\n" + - "\tinfile - A file of chromosome-positions, tab-delimited\n" + - "\tOPTIONS\n" + - "\t--positions-file - a file of chromosome-positions, tab delimited, or VCF\n" + ---- a/net/sf/varscan/ProcessSomatic.java -+++ b/net/sf/varscan/ProcessSomatic.java -@@ -19,7 +19,7 @@ public class ProcessSomatic { - - public ProcessSomatic(String[] args) - { -- String usage = "USAGE: java -jar VarScan.jar process [status-file] OPTIONS\n" + -+ String usage = "USAGE: varscan process [status-file] OPTIONS\n" + - "\tstatus-file - The VarScan output file for SNPs or Indels\n" + - "\tOPTIONS\n" + - "\t--min-tumor-freq - Minimum variant allele frequency in tumor [0.10]\n" + ---- a/net/sf/varscan/ReadCounts.java -+++ b/net/sf/varscan/ReadCounts.java -@@ -28,7 +28,7 @@ public class ReadCounts { - - public ReadCounts(String[] args, HashMap<String, String> params) - { -- String usage = "USAGE: java -jar VarScan.jar readcounts [pileup] OPTIONS\n" + -+ String usage = "USAGE: varscan readcounts [pileup] OPTIONS\n" + - "\tOPTIONS:\n" + - "\t--variants-file\tA list of variants at which to report readcounts\n" + - "\t--output-file\tOutput file to contain the readcounts\n" + ---- a/net/sf/varscan/Somatic.java -+++ b/net/sf/varscan/Somatic.java -@@ -34,7 +34,7 @@ public class Somatic { - - public Somatic(String[] args, boolean isMpileup) - { -- String usage = "USAGE: java -jar VarScan.jar somatic [normal-tumor.mpileup] [Opt: output] OPTIONS\n" + -+ String usage = "USAGE: varscan somatic [normal-tumor.mpileup] [Opt: output] OPTIONS\n" + - "\tnormal-tumor.pileup - The SAMtools mpileup file for Normal and Tumor BAMs\n" + - "\toutput - Output base name for SNP and indel output\n" + - "\nOPTIONS:\n" + ---- a/net/sf/varscan/Trio.java -+++ b/net/sf/varscan/Trio.java -@@ -29,7 +29,7 @@ public class Trio { - public Trio(String[] args, String callType) - { - // Define the usage message // -- String usage = "USAGE: java -jar VarScan.jar trio [mpileup file] [output-basename] OPTIONS\n" + -+ String usage = "USAGE: varscan trio [mpileup file] [output-basename] OPTIONS\n" + - "\tmpileup file - The SAMtools mpileup file for father, mother, child in that order\n" + - "\n" + - "\tOPTIONS:\n" + ---- a/net/sf/varscan/VarScan.java -+++ b/net/sf/varscan/VarScan.java -@@ -105,7 +105,7 @@ public class VarScan { - */ - public static void main(String[] args) { - -- String usage = "VarScan v2.3\n\nUSAGE: java -jar VarScan.jar [COMMAND] [OPTIONS] \n\n"; -+ String usage = "VarScan v2.3\n\nUSAGE: varscan [COMMAND] [OPTIONS] \n\n"; - usage = usage + "COMMANDS:\n" + - "\tpileup2snp\t\tIdentify SNPs from a pileup file\n" + - "\tpileup2indel\t\tIdentify indels a pileup file\n" + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/varscan.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
