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Resolving merge conflicts

This commit is contained in:
Eric Banks 2012-04-12 15:19:44 -04:00
parent 4004ec3e6f 0dd571928d
commit 818e8c2fb9
3 changed files with 13 additions and 17 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
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@ -36,10 +36,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import java.util.*; import java.util.*;
@ -273,16 +270,15 @@ public class ConsensusAlleleCounter {
builder.alleles(Arrays.asList(refAllele, altAllele)); builder.alleles(Arrays.asList(refAllele, altAllele));
builder.referenceBaseForIndel(ref.getBase()); builder.referenceBaseForIndel(ref.getBase());
builder.noGenotypes(); builder.noGenotypes();
if (doMultiAllelicCalls) if (doMultiAllelicCalls) {
vcs.add(builder.make()); vcs.add(builder.make());
else { if (vcs.size() >= GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
if (curCnt > maxAlleleCnt) { break;
} else if (curCnt > maxAlleleCnt) {
maxAlleleCnt = curCnt; maxAlleleCnt = curCnt;
vcs.clear(); vcs.clear();
vcs.add(builder.make()); vcs.add(builder.make());
} }
}
} }
if (vcs.isEmpty()) if (vcs.isEmpty())

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -217,8 +217,8 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
**/ **/
public void initialize() { public void initialize() {
// check for a bad max alleles value // check for a bad max alleles value
if ( UAC.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_ALLELES_THAT_CAN_BE_GENOTYPED ) if ( UAC.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_ALLELES_THAT_CAN_BE_GENOTYPED); throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED);
// warn the user for misusing EMIT_ALL_SITES // warn the user for misusing EMIT_ALL_SITES
if ( UAC.OutputMode == UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES && if ( UAC.OutputMode == UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES &&

6
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
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@ -223,12 +223,12 @@ public class GenotypeLikelihoods {
/** /**
* The maximum number of alleles that we can represent as genotype likelihoods * The maximum number of alleles that we can represent as genotype likelihoods
*/ */
public final static int MAX_ALLELES_THAT_CAN_BE_GENOTYPED = 50; public final static int MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED = 50;
/* /*
* a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles * a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles
*/ */
private final static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = calculatePLcache(MAX_ALLELES_THAT_CAN_BE_GENOTYPED); private final static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = calculatePLcache(MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED);
private static GenotypeLikelihoodsAllelePair[] calculatePLcache(final int altAlleles) { private static GenotypeLikelihoodsAllelePair[] calculatePLcache(final int altAlleles) {
final int numLikelihoods = calculateNumLikelihoods(1+altAlleles, 2); final int numLikelihoods = calculateNumLikelihoods(1+altAlleles, 2);
@ -311,7 +311,7 @@ public class GenotypeLikelihoods {
public static GenotypeLikelihoodsAllelePair getAllelePair(final int PLindex) { public static GenotypeLikelihoodsAllelePair getAllelePair(final int PLindex) {
// make sure that we've cached enough data // make sure that we've cached enough data
if ( PLindex >= PLIndexToAlleleIndex.length ) if ( PLindex >= PLIndexToAlleleIndex.length )
throw new ReviewedStingException("GATK limitation: cannot genotype more than " + MAX_ALLELES_THAT_CAN_BE_GENOTYPED + " alleles"); throw new ReviewedStingException("GATK limitation: cannot genotype more than " + MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED + " alleles");
return PLIndexToAlleleIndex[PLindex]; return PLIndexToAlleleIndex[PLindex];
} }