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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-05-10 13:09:10 -04:00
parent 0cdadffe14 89f8a6b2e6
commit c9dd0f3173
4 changed files with 36 additions and 8 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -21,7 +21,7 @@ import java.util.List;
import java.util.Map;
/**
* Variant confidence (given as (AB+BB)/AA from the PLs) / unfiltered depth.
* Variant confidence (from the QUAL field) / unfiltered depth.
*
* Low scores are indicative of false positive calls and artifacts. Note that QualByDepth requires sequencing
* reads associated with the samples with polymorphic genotypes.
@ -100,4 +100,4 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
return map;
}
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
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@ -253,14 +253,14 @@ public class ConsensusAlleleCounter {
stop = loc.getStart() + dLen;
final byte[] refBases = Arrays.copyOfRange(ref.getBases(), startIdxInReference, startIdxInReference + dLen);
if (Allele.acceptableAlleleBases(refBases)) {
if (Allele.acceptableAlleleBases(refBases, false)) {
refAllele = Allele.create(refBases, true);
altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false);
}
else continue; // don't go on with this allele if refBases are non-standard
} else {
// insertion case
if (Allele.acceptableAlleleBases(s)) {
if (Allele.acceptableAlleleBases(s, false)) { // don't allow N's in insertions
refAllele = Allele.create(Allele.NULL_ALLELE_STRING, true);
altAllele = Allele.create(s, false);
stop = loc.getStart();

21
public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
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@ -226,7 +226,11 @@ public class Allele implements Comparable<Allele> {
* @return true if the bases represent the well formatted allele
*/
public static boolean acceptableAlleleBases(String bases) {
return acceptableAlleleBases(bases.getBytes());
return acceptableAlleleBases(bases.getBytes(), true);
}
public static boolean acceptableAlleleBases(String bases, boolean allowNsAsAcceptable) {
return acceptableAlleleBases(bases.getBytes(), allowNsAsAcceptable);
}
/**
@ -234,13 +238,22 @@ public class Allele implements Comparable<Allele> {
* @return true if the bases represent the well formatted allele
*/
public static boolean acceptableAlleleBases(byte[] bases) {
return acceptableAlleleBases(bases, true); // default: N bases are acceptable
}
public static boolean acceptableAlleleBases(byte[] bases, boolean allowNsAsAcceptable) {
if ( wouldBeNullAllele(bases) || wouldBeNoCallAllele(bases) || wouldBeSymbolicAllele(bases) )
return true;
for ( int i = 0; i < bases.length; i++ ) {
switch (bases[i]) {
case 'A': case 'C': case 'G': case 'T': case 'N' : case 'a': case 'c': case 'g': case 't': case 'n' :
for (byte base : bases ) {
switch (base) {
case 'A': case 'C': case 'G': case 'T': case 'a': case 'c': case 'g': case 't':
break;
case 'N' : case 'n' :
if (allowNsAsAcceptable)
break;
else
return false;
default:
return false;
}

15
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
View File

@ -90,6 +90,21 @@ public class IndelGenotypeLikelihoodsUnitTest extends BaseTest {
Assert.assertEquals(alleles.size(),2);
alleles = getConsensusAlleles(eventLength,false,10,0.5001, altBases);
Assert.assertEquals(alleles.size(),0);
// test N's in insertions
altBases = "CCTCNTGAGA";
eventLength = 4;
alleles = getConsensusAlleles(eventLength,true,10,0.1, altBases);
Assert.assertEquals(alleles.size(),2);
Assert.assertEquals(alleles.get(1).getBaseString(), altBases.substring(0,eventLength));
altBases = "CCTCNTGAGA";
eventLength = 5;
alleles = getConsensusAlleles(eventLength,true,10,0.1, altBases);
Assert.assertEquals(alleles.size(),0);
}
private List<Allele> getConsensusAlleles(int eventLength, boolean isInsertion, int minCnt, double minFraction, String altBases) {