From f3ac5d404dc50ba89229cb07dba118f42f6956a6 Mon Sep 17 00:00:00 2001 From: Andrey Sivachenko Date: Fri, 26 Oct 2012 23:52:21 -0400 Subject: [PATCH] updating vcf header attribute descriptions in order to reflect correctly what's actually being written... --- .../gatk/walkers/indels/SomaticIndelDetector.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java index be668b9c3..0165c6cf3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java @@ -2196,16 +2196,16 @@ class VCFIndelAttributes { public static Set getAttributeHeaderLines() { Set lines = new HashSet(); - lines.add(new VCFFormatHeaderLine(ALLELIC_DEPTH_KEY, 2, VCFHeaderLineType.Integer, "# of reads supporting consensus indel/reference at the site")); + lines.add(new VCFFormatHeaderLine(ALLELIC_DEPTH_KEY, 2, VCFHeaderLineType.Integer, "# of reads supporting consensus reference/indel at the site")); lines.add(new VCFFormatHeaderLine(DEPTH_TOTAL_KEY, 1, VCFHeaderLineType.Integer, "Total coverage at the site")); - lines.add(new VCFFormatHeaderLine(MAPQ_KEY, 2, VCFHeaderLineType.Float, "Average mapping qualities of consensus indel-supporting reads/reference-supporting reads")); + lines.add(new VCFFormatHeaderLine(MAPQ_KEY, 2, VCFHeaderLineType.Float, "Average mapping qualities of ref-/consensus indel-supporting reads")); - lines.add(new VCFFormatHeaderLine(MM_KEY, 2, VCFHeaderLineType.Float, "Average # of mismatches per consensus indel-supporting read/per reference-supporting read")); + lines.add(new VCFFormatHeaderLine(MM_KEY, 2, VCFHeaderLineType.Float, "Average # of mismatches per ref-/consensus indel-supporting read")); - lines.add(new VCFFormatHeaderLine(NQS_MMRATE_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: fraction of mismatching bases in consensus indel-supporting reads/in reference-supporting reads")); + lines.add(new VCFFormatHeaderLine(NQS_MMRATE_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: fraction of mismatching bases in ref/consensus indel-supporting reads")); - lines.add(new VCFFormatHeaderLine(NQS_AVQ_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: average quality of bases from consensus indel-supporting reads/from reference-supporting reads")); + lines.add(new VCFFormatHeaderLine(NQS_AVQ_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: average quality of bases in ref-/consensus indel-supporting reads")); lines.add(new VCFFormatHeaderLine(STRAND_COUNT_KEY, 4, VCFHeaderLineType.Integer, "Strandness: counts of forward-/reverse-aligned reference and indel-supporting reads (FwdRef,RevRef,FwdIndel,RevIndel)"));