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Merge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Guillermo del Angel 2012-10-31 14:17:41 -04:00
parent 4580e99c0c 96344c6b62
commit 24e6da25cc
1 changed files with 2 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -236,6 +236,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
* then extensions (".bam" or ".sam") will be stripped from the input file names and the provided string value will be pasted on instead; 2) if the * then extensions (".bam" or ".sam") will be stripped from the input file names and the provided string value will be pasted on instead; 2) if the
* value ends with a '.map' (e.g. input_output.map), then the two-column tab-separated file with the specified name must exist and list unique output * value ends with a '.map' (e.g. input_output.map), then the two-column tab-separated file with the specified name must exist and list unique output
* file name (2nd column) for each input file name (1st column). * file name (2nd column) for each input file name (1st column).
*
* Note that some GATK arguments do NOT work in conjunction with nWayOut (e.g. --disable_bam_indexing).
*/ */
@Argument(fullName="nWayOut", shortName="nWayOut", required=false, doc="Generate one output file for each input (-I) bam file") @Argument(fullName="nWayOut", shortName="nWayOut", required=false, doc="Generate one output file for each input (-I) bam file")
protected String N_WAY_OUT = null; protected String N_WAY_OUT = null;