[med-svn] [varscan] 01/01: Adapt usage message
Andreas Tille
tille at debian.org
Thu Apr 17 08:50:08 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository varscan.
commit 93705fcb87f065bc6fe904b27d906bab296f3ceb
Author: Andreas Tille <tille at debian.org>
Date: Thu Apr 17 10:44:12 2014 +0200
Adapt usage message
---
debian/patches/{fix_convert => fix_convert.patch} | 4 +-
debian/patches/series | 3 +-
debian/patches/usage.patch | 159 ++++++++++++++++++++++
3 files changed, 163 insertions(+), 3 deletions(-)
diff --git a/debian/patches/fix_convert b/debian/patches/fix_convert.patch
similarity index 89%
rename from debian/patches/fix_convert
rename to debian/patches/fix_convert.patch
index adcb07c..fd6f8c4 100644
--- a/debian/patches/fix_convert
+++ b/debian/patches/fix_convert.patch
@@ -5,7 +5,7 @@ Forwarded: no
Last-Updated: 2014-04-17
--- a/net/sf/varscan/CopyCaller.java
+++ b/net/sf/varscan/CopyCaller.java
-@@ -253,7 +253,7 @@
+@@ -253,7 +253,7 @@ public class CopyCaller {
int gcBin = (int) gcContent;
if(gcBin >= 0 && gcBin <= 100)
{
@@ -14,7 +14,7 @@ Last-Updated: 2014-04-17
gcLogNum[gcBin]++;
}
}
-@@ -576,4 +576,4 @@
+@@ -576,4 +576,4 @@ public class CopyCaller {
return(regionRef + "\t" + regionStart + "\t" + regionStop + "\t" + regionCalls + "\t" + regionDepthNormal + "\t" + regionDepthTumor + "\t" + log2ratio);
}
diff --git a/debian/patches/series b/debian/patches/series
index 7dd2fe9..ff6eedb 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
-fix_convert
+fix_convert.patch
+usage.patch
diff --git a/debian/patches/usage.patch b/debian/patches/usage.patch
new file mode 100644
index 0000000..1777246
--- /dev/null
+++ b/debian/patches/usage.patch
@@ -0,0 +1,159 @@
+Author: Andreas Tille <tille at debian.org>
+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" +
--
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