From b8cdf64c20fab07958a5e54f84067b8aadb81f44 Mon Sep 17 00:00:00 2001 From: ebanks Date: Sun, 17 Jan 2010 02:30:27 +0000 Subject: [PATCH] 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 --- .../sting/gatk/arguments/GATKArgumentCollection.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index fcdd71592..2e12a61f2 100755 --- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -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)