From d7499e0642519d6e0b56fd74ba684f4de9bbfc91 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sun, 9 Sep 2012 22:17:36 -0400 Subject: [PATCH] Updating the rank sum test documentation --- .../sting/gatk/walkers/annotator/BaseQualityRankSumTest.java | 2 +- .../sting/gatk/walkers/annotator/ClippingRankSumTest.java | 4 ++++ .../gatk/walkers/annotator/MappingQualityRankSumTest.java | 2 +- .../sting/gatk/walkers/annotator/ReadPosRankSumTest.java | 2 +- 4 files changed, 7 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 dc727fa48..577b1cfdc 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 @@ -16,7 +16,7 @@ import java.util.*; /** * 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. + * Note that the base quality rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles. */ public class BaseQualityRankSumTest extends RankSumTest implements StandardAnnotation { public List getKeyNames() { return Arrays.asList("BaseQRankSum"); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java index 1fd220f2f..c74f98ca3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java @@ -16,6 +16,10 @@ import java.util.*; * Date: 6/28/12 */ +/** + * The u-based z-approximation from the Mann-Whitney Rank Sum Test for reads with clipped bases (reads with ref bases vs. those with the alternate allele) + * Note that the clipping rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles. + */ public class ClippingRankSumTest extends RankSumTest { public List getKeyNames() { return Arrays.asList("ClippingRankSum"); } 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 6557f3e47..787c9b29b 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 @@ -17,7 +17,7 @@ import java.util.*; /** * 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. + * Note that the mapping quality rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles. */ public class MappingQualityRankSumTest extends RankSumTest implements StandardAnnotation { 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 1ac8ee113..de0ce2ce2 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 @@ -20,7 +20,7 @@ import java.util.*; /** * 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. + * Note that the read position rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles. */ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotation {