From 341d1bf2dd220a70f3b0cef13ab34e046d97211c Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 19 Feb 2014 20:42:08 -0500 Subject: [PATCH] Fix the usage message for CatVariants to make it accurate. It just hit a user on our forum... --- .../org/broadinstitute/sting/tools/CatVariants.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java index 8e5078f1f..1dc5f8516 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java @@ -136,11 +136,11 @@ public class CatVariants extends CommandLineProgram { * print usage information */ private static void printUsage() { - System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants [sorted (optional)]"); - System.err.println(" The input files can be of type: VCF (ends in .vcf or .VCF)"); - System.err.println(" BCF2 (ends in .bcf or .BCF)"); - System.err.println(" Output file must be vcf or bcf file (.vcf or .bcf)"); - System.err.println(" if the input files are already sorted, the last argument can indicate that"); + System.err.println("Usage: java -cp target/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants --reference --variant --outputFile [--assumeSorted]"); + System.err.println(" The input file(s) can be of type: VCF (must end in .vcf or .VCF) or"); + System.err.println(" BCF2 (must end in .bcf or .BCF)."); + System.err.println(" Output file must be of type vcf or bcf (must end in .vcf or .bcf)."); + System.err.println(" If the input files are already sorted, then indicate that with --assumeSorted to improve performance."); } @Override