Author: Andreas Tille <tille@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" +
