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Merge pull request #726 from broadinstitute/rp_haplotypeCaller_typo_fix 

fixing a few small typos in the HaplotypeCaller and related classes
This commit is contained in:
rpoplin 2014-09-04 15:04:41 -04:00
parent f53ea3b456 1b809268d5
commit 9705df2f7a
3 changed files with 9 additions and 9 deletions
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4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java
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@ -599,7 +599,7 @@ public class GenotypeAlleleCounts implements Comparable<GenotypeAlleleCounts>, C
} }
// It is guaranteed that at this point alleleIndex == nextIndex // It is guaranteed that at this point alleleIndex == nextIndex
// thanks to the condition of the enclosing while: there must be at least one index of interest that // thanks to the condition of the enclosing while: there must be at least one index of interest that
// it is present in remaning (nextRank,endRank] interval as otherwise endRank would be less than nextRank. // is present in the remaining (nextRank,endRank] interval as otherwise endRank would be less than nextRank.
dest[nextDestOffset++] = sortedAlleleCounts[nextSortedAlleleCountsOffset++]; dest[nextDestOffset++] = sortedAlleleCounts[nextSortedAlleleCountsOffset++];
nextIndex++; nextIndex++;
} }
@ -756,7 +756,7 @@ public class GenotypeAlleleCounts implements Comparable<GenotypeAlleleCounts>, C
* </p> * </p>
* *
* <p> * <p>
* If a sufficiently large array is provided as {@code dest}, this is used as the destination. Unecessary * If a sufficiently large array is provided as {@code dest}, this is used as the destination. Unnecessary
* positions at the back of the array are left untouched. * positions at the back of the array are left untouched.
* </p> * </p>
* *

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
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@ -245,7 +245,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
final LinkedList<ExactACset> ACqueue, final LinkedList<ExactACset> ACqueue,
final HashMap<ExactACcounts, ExactACset> indexesToACset) { final HashMap<ExactACcounts, ExactACset> indexesToACset) {
// compute likeihood in "set" of new set based on original likelihoods // compute likelihood in "set" of new set based on original likelihoods
final int numAlleles = set.getACcounts().getCounts().length; final int numAlleles = set.getACcounts().getCounts().length;
final int newPloidy = set.getACsum(); final int newPloidy = set.getACsum();
final double log10LofK = computeLofK(set, originalPool, newGL, log10AlleleFrequencyPriors, numAlleles, originalPloidy, newGLPloidy); final double log10LofK = computeLofK(set, originalPool, newGL, log10AlleleFrequencyPriors, numAlleles, originalPloidy, newGLPloidy);
@ -358,7 +358,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
* @param numAlleles Number of alleles (including ref) * @param numAlleles Number of alleles (including ref)
* @param ploidy1 Ploidy of original pool (combined) * @param ploidy1 Ploidy of original pool (combined)
* @param ploidy2 Ploidy of new pool * @param ploidy2 Ploidy of new pool
* @return log-likehood of requested conformation * @return log-likelihood of requested conformation
*/ */
private double computeLofK(final ExactACset set, private double computeLofK(final ExactACset set,
final CombinedPoolLikelihoods firstGLs, final CombinedPoolLikelihoods firstGLs,
@ -441,7 +441,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
} }
/** /**
* Small helper routine - is a particular AC conformationv vector valid? ie are all elements non-negative and sum to ploidy? * Small helper routine - is a particular AC conformation vector valid? ie are all elements non-negative and sum to ploidy?
* @param set AC conformation vector * @param set AC conformation vector
* @param ploidy Ploidy of set * @param ploidy Ploidy of set
* @return Valid conformation * @return Valid conformation

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -243,7 +243,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
@Hidden @Hidden
@Advanced @Advanced
@Argument(fullName="heterogeneousKmerSizeResolution",shortName="hksr",doc="how to solve heterogeneous kmer situations using the fast method",required=false) @Argument(fullName="heterogeneousKmerSizeResolution",shortName="hksr",doc="how to solve heterogeneous kmer situations using the fast method",required=false)
protected HeterogeneousKmerSizeResolution heterogeneousKmerSizeResultion = HeterogeneousKmerSizeResolution.COMBO_MIN; protected HeterogeneousKmerSizeResolution heterogeneousKmerSizeResolution = HeterogeneousKmerSizeResolution.COMBO_MIN;
@Output(fullName="graphOutput", shortName="graph", doc="File to which debug assembly graph information should be written", required = false, defaultToStdout = false) @Output(fullName="graphOutput", shortName="graph", doc="File to which debug assembly graph information should be written", required = false, defaultToStdout = false)
protected PrintStream graphWriter = null; protected PrintStream graphWriter = null;
@ -822,7 +822,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
case PairHMM: case PairHMM:
return new PairHMMLikelihoodCalculationEngine( (byte)gcpHMM, pairHMM, log10GlobalReadMismappingRate, noFpga, pcrErrorModel ); return new PairHMMLikelihoodCalculationEngine( (byte)gcpHMM, pairHMM, log10GlobalReadMismappingRate, noFpga, pcrErrorModel );
case GraphBased: case GraphBased:
return new GraphBasedLikelihoodCalculationEngine( (byte)gcpHMM,log10GlobalReadMismappingRate,heterogeneousKmerSizeResultion,SCAC.DEBUG,debugGraphTransformations); return new GraphBasedLikelihoodCalculationEngine( (byte)gcpHMM,log10GlobalReadMismappingRate, heterogeneousKmerSizeResolution,SCAC.DEBUG,debugGraphTransformations);
case Random: case Random:
return new RandomLikelihoodCalculationEngine(); return new RandomLikelihoodCalculationEngine();
default: default:
@ -931,7 +931,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
final AssemblyResultSet untrimmedAssemblyResult = assembleReads(originalActiveRegion, givenAlleles); final AssemblyResultSet untrimmedAssemblyResult = assembleReads(originalActiveRegion, givenAlleles);
final TreeSet<VariantContext> allVariationEvents = untrimmedAssemblyResult.getVariationEvents(); final TreeSet<VariantContext> allVariationEvents = untrimmedAssemblyResult.getVariationEvents();
// TODO - line bellow might be unecessary : it might be that assemblyResult will always have those alleles anyway // TODO - line bellow might be unnecessary : it might be that assemblyResult will always have those alleles anyway
// TODO - so check and remove if that is the case: // TODO - so check and remove if that is the case:
allVariationEvents.addAll(givenAlleles); allVariationEvents.addAll(givenAlleles);
@ -973,7 +973,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
final List<Haplotype> haplotypes = assemblyResult.getHaplotypeList(); final List<Haplotype> haplotypes = assemblyResult.getHaplotypeList();
final Map<String,List<GATKSAMRecord>> reads = splitReadsBySample( regionForGenotyping.getReads() ); final Map<String,List<GATKSAMRecord>> reads = splitReadsBySample( regionForGenotyping.getReads() );
// Calculate the likelihoods: CPU intesive part. // Calculate the likelihoods: CPU intensive part.
final ReadLikelihoods<Haplotype> readLikelihoods = final ReadLikelihoods<Haplotype> readLikelihoods =
likelihoodCalculationEngine.computeReadLikelihoods(assemblyResult,samplesList,reads); likelihoodCalculationEngine.computeReadLikelihoods(assemblyResult,samplesList,reads);