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Mapping and base quality thresholds for DoC default to none 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3326 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-05-07 18:08:13 +00:00
parent 7d2df3f511
commit 1749a49042
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -82,9 +82,9 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<String,int[]>, Covera
@Argument(fullName = "nBins", doc = "Number of bins to use for granular binning", required = false)
int nBins = 499;
@Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth. Defaults to 50.", required = false)
byte minMappingQuality = 50;
byte minMappingQuality = -1;
@Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth. Defaults to 20.", required = false)
byte minBaseQuality = 20;
byte minBaseQuality = -1;
@Argument(fullName = "printBaseCounts", shortName = "baseCounts", doc = "Will add base counts to per-locus output.", required = false)
boolean printBaseCounts = false;
@Argument(fullName = "omitLocusTable", shortName = "omitLocusTable", doc = "Will not calculate the per-sample per-depth counts of loci, which should result in speedup", required = false)