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Better descriptions for max reads/downsampling args 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2618 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-01-17 02:30:27 +00:00
parent aa08c82ac0
commit b8cdf64c20
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -112,7 +112,7 @@ public class GATKArgumentCollection {
public Double downsampleFraction = null;
@Element(required = false)
@Argument(fullName = "downsample_to_coverage", shortName = "dcov", doc = "Coverage [integer] to downsample to", required = false)
@Argument(fullName = "downsample_to_coverage", shortName = "dcov", doc = "Coverage [integer] to downsample to at any given locus; note that downsampled reads are randomly selected from all possible reads at a locus (use max_reads_at_locus to stop the engine from reading in all reads)", required = false)
public Integer downsampleCoverage = null;
@Element(required = false)
@ -124,7 +124,7 @@ public class GATKArgumentCollection {
public ValidationExclusion.TYPE unsafe;
@Element(required = false)
@Argument(fullName = "max_reads_at_locus", shortName = "mrl", doc = "Sets the upper limit for the number of reads presented at a single locus. int.MAX_VALUE by default.", required = false)
@Argument(fullName = "max_reads_at_locus", shortName = "mrl", doc = "Sets the upper limit for the number of reads presented at a single locus; use this argument if you are running into memory issues resulting from too many reads piled up at a given locus (but use downsample_to_coverage instead if you are trying to downsample); int.MAX_VALUE by default.", required = false)
public int readMaxPileup = Integer.MAX_VALUE;
@Element(required = false)