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Fixing docs (rank sum test values are not phred-scaled)

This commit is contained in:
Eric Banks 2012-04-24 09:39:42 -04:00
parent a733723439
commit bcb93dda5f
3 changed files with 3 additions and 3 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
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@ -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. * Note that the base quality rank sum test can not be calculated for homozygous sites.
*/ */
public class BaseQualityRankSumTest extends RankSumTest { public class BaseQualityRankSumTest extends RankSumTest {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
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@ -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. * Note that the mapping quality rank sum test can not be calculated for homozygous sites.
*/ */
public class MappingQualityRankSumTest extends RankSumTest { public class MappingQualityRankSumTest extends RankSumTest {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
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@ -18,7 +18,7 @@ import org.broadinstitute.sting.utils.variantcontext.Allele;
import java.util.*; 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. * Note that the read position rank sum test can not be calculated for homozygous sites.
*/ */
public class ReadPosRankSumTest extends RankSumTest { public class ReadPosRankSumTest extends RankSumTest {