From bcb93dda5f19225ac642e1ee5af198194a956414 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 24 Apr 2012 09:39:42 -0400 Subject: [PATCH] Fixing docs (rank sum test values are not phred-scaled) --- .../sting/gatk/walkers/annotator/BaseQualityRankSumTest.java | 2 +- .../sting/gatk/walkers/annotator/MappingQualityRankSumTest.java | 2 +- .../sting/gatk/walkers/annotator/ReadPosRankSumTest.java | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java index 526f25797..8bc5f06f4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java @@ -12,7 +12,7 @@ import java.util.*; /** - * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele). + * The u-based z-approximation from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele). * Note that the base quality rank sum test can not be calculated for homozygous sites. */ public class BaseQualityRankSumTest extends RankSumTest { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java index 749278ce7..4ce19e824 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java @@ -13,7 +13,7 @@ import java.util.*; /** - * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases vs. those with the alternate allele) + * The u-based z-approximation from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases vs. those with the alternate allele) * Note that the mapping quality rank sum test can not be calculated for homozygous sites. */ public class MappingQualityRankSumTest extends RankSumTest { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index 9ff8886cf..92e6f8536 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java @@ -18,7 +18,7 @@ import org.broadinstitute.sting.utils.variantcontext.Allele; import java.util.*; /** - * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele; if the alternate allele is only seen near the ends of reads this is indicative of error). + * The u-based z-approximation from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele; if the alternate allele is only seen near the ends of reads this is indicative of error). * Note that the read position rank sum test can not be calculated for homozygous sites. */ public class ReadPosRankSumTest extends RankSumTest {