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Merge pull request #528 from broadinstitute/eb_fix_cat_variants_usage_message 

Fix the usage message for CatVariants to make it accurate.
This commit is contained in:
Eric Banks 2014-02-19 22:45:22 -05:00
parent 6edebcb4ce 341d1bf2dd
commit 235f0c6fa0
1 changed files with 5 additions and 5 deletions
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10
public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java
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@ -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 <reference> <input VCF or BCF files> <outputFile> [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 <reference> --variant <input VCF or BCF file; can specify --variant multiple times> --outputFile <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