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Updating the rank sum test documentation

This commit is contained in:
Eric Banks 2012-09-09 22:17:36 -04:00
parent 3dd0f59765
commit d7499e0642
4 changed files with 7 additions and 3 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
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@ -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). * 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 class BaseQualityRankSumTest extends RankSumTest implements StandardAnnotation {
public List<String> getKeyNames() { return Arrays.asList("BaseQRankSum"); } public List<String> getKeyNames() { return Arrays.asList("BaseQRankSum"); }

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
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@ -16,6 +16,10 @@ import java.util.*;
* Date: 6/28/12 * 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 class ClippingRankSumTest extends RankSumTest {
public List<String> getKeyNames() { return Arrays.asList("ClippingRankSum"); } public List<String> getKeyNames() { return Arrays.asList("ClippingRankSum"); }

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
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@ -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) * 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 { public class MappingQualityRankSumTest extends RankSumTest implements StandardAnnotation {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
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@ -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). * 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 { public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotation {