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Merge pull request #863 from broadinstitute/kc_m2_initial_commit 

Seeking comments on visibility changes to HaplotypeCaller-related classes

Welcome to GATK-master, MuTect2!
This commit is contained in:
Geraldine Van der Auwera 2015-03-13 21:05:39 -04:00
parent 1d39ed9156 ab1053e83c
commit 517320092c
5 changed files with 30 additions and 19 deletions
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8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTrimmer.java
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@ -72,7 +72,7 @@ import java.util.*;
*
* @author Valentin Ruano-Rubio <valentin@broadinstitute.org>
*/
class ActiveRegionTrimmer {
public class ActiveRegionTrimmer {
/**
* Genome location parser use in order to create and manipulate genomic intervals.
@ -115,11 +115,11 @@ class ActiveRegionTrimmer {
*/
@Hidden
@Argument(fullName="paddingAroundIndels", shortName="paddingAroundIndels", doc = "Include at least this many bases around an event for calling indels", required=false)
protected int indelPadding = 150;
public int indelPadding = 150;
@Hidden
@Argument(fullName="paddingAroundSNPs", shortName="paddingAroundSNPs", doc = "Include at least this many bases around an event for calling snps", required=false)
protected int snpPadding = 20;
public int snpPadding = 20;
/**
* Holds a reference the trimmer logger.
@ -143,7 +143,7 @@ class ActiveRegionTrimmer {
* @throws IllegalArgumentException if the input location parser is {@code null}.
* @throws UserException.BadArgumentValue if any of the user argument values is invalid.
*/
void initialize(final GenomeLocParser glp, final boolean debug, final boolean isGGA, final boolean emitReferenceConfidence) {
public void initialize(final GenomeLocParser glp, final boolean debug, final boolean isGGA, final boolean emitReferenceConfidence) {
if (locParser != null)
throw new IllegalStateException(getClass().getSimpleName() + " instance initialized twice");
if (glp == null)

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -1360,7 +1360,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
return splitReadsBySample(samplesList, reads);
}
private static Map<String, List<GATKSAMRecord>> splitReadsBySample( final SampleList samplesList, final Collection<GATKSAMRecord> reads ) {
public static Map<String, List<GATKSAMRecord>> splitReadsBySample( final SampleList samplesList, final Collection<GATKSAMRecord> reads ) {
final Map<String, List<GATKSAMRecord>> returnMap = new HashMap<>();
final int sampleCount = samplesList.sampleCount();
for (int i = 0; i < sampleCount; i++)

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
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@ -64,11 +64,11 @@ public class HaplotypeCallerArgumentCollection extends StandardCallerArgumentCol
@Advanced
@Argument(fullName="debug", shortName="debug", doc="Print out very verbose debug information about each triggering active region", required = false)
protected boolean DEBUG;
public boolean DEBUG;
@Advanced
@Argument(fullName="useFilteredReadsForAnnotations", shortName="useFilteredReadsForAnnotations", doc = "Use the contamination-filtered read maps for the purposes of annotating variants", required=false)
protected boolean USE_FILTERED_READ_MAP_FOR_ANNOTATIONS = false;
public boolean USE_FILTERED_READ_MAP_FOR_ANNOTATIONS = false;
/**
* The reference confidence mode makes it possible to emit a per-bp or summarized confidence estimate for a site being strictly homozygous-reference.

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
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@ -78,7 +78,7 @@ import java.util.*;
*/
public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeCallerArgumentCollection> {
private static final int ALLELE_EXTENSION = 2;
protected static final int ALLELE_EXTENSION = 2;
private static final String phase01 = "0|1";
private static final String phase10 = "1|0";
@ -139,7 +139,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
private final List<VariantContext> calls;
private final Set<Haplotype> calledHaplotypes;
protected CalledHaplotypes(final List<VariantContext> calls, final Set<Haplotype> calledHaplotypes) {
public CalledHaplotypes(final List<VariantContext> calls, final Set<Haplotype> calledHaplotypes) {
if ( calls == null ) throw new IllegalArgumentException("calls cannot be null");
if ( calledHaplotypes == null ) throw new IllegalArgumentException("calledHaplotypes cannot be null");
if ( Utils.xor(calls.isEmpty(), calledHaplotypes.isEmpty()) )
@ -531,7 +531,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
// Builds the read-likelihoods collection to use for annotation considering user arguments and the collection
// used for genotyping.
private ReadLikelihoods<Allele> prepareReadAlleleLikelihoodsForAnnotation(
protected ReadLikelihoods<Allele> prepareReadAlleleLikelihoodsForAnnotation(
final ReadLikelihoods<Haplotype> readHaplotypeLikelihoods,
final Map<String, List<GATKSAMRecord>> perSampleFilteredReadList,
final GenomeLocParser genomeLocParser,
@ -596,7 +596,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
* @param activeAllelesToGenotype alleles we want to ensure are scheduled for genotyping (GGA mode)
* @return never {@code null} but perhaps an empty list if there is no variants to report.
*/
private TreeSet<Integer> decomposeHaplotypesIntoVariantContexts(final List<Haplotype> haplotypes,
protected TreeSet<Integer> decomposeHaplotypesIntoVariantContexts(final List<Haplotype> haplotypes,
final ReadLikelihoods readLikelihoods,
final byte[] ref,
final GenomeLoc refLoc,
@ -628,13 +628,13 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
* @param vcs a list of variant contexts
* @return the list of the sources of vcs in the same order
*/
private List<String> makePriorityList(final List<VariantContext> vcs) {
protected List<String> makePriorityList(final List<VariantContext> vcs) {
final List<String> priorityList = new LinkedList<>();
for ( final VariantContext vc : vcs ) priorityList.add(vc.getSource());
return priorityList;
}
private List<VariantContext> getVCsAtThisLocation(final List<Haplotype> haplotypes,
protected List<VariantContext> getVCsAtThisLocation(final List<Haplotype> haplotypes,
final int loc,
final List<VariantContext> activeAllelesToGenotype) {
// the overlapping events to merge into a common reference view
@ -687,7 +687,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
*/
@Requires({"readLikelihoods!= null", "mergedVC != null"})
@Ensures("result != null")
private GenotypesContext calculateGLsForThisEvent( final ReadLikelihoods<Allele> readLikelihoods, final VariantContext mergedVC, final List<Allele> noCallAlleles ) {
protected GenotypesContext calculateGLsForThisEvent( final ReadLikelihoods<Allele> readLikelihoods, final VariantContext mergedVC, final List<Allele> noCallAlleles ) {
final List<Allele> vcAlleles = mergedVC.getAlleles();
final AlleleList<Allele> alleleList = readLikelihoods.alleleCount() == vcAlleles.size() ? readLikelihoods : new IndexedAlleleList<>(vcAlleles);
final GenotypingLikelihoods<Allele> likelihoods = genotypingModel.calculateLikelihoods(alleleList,new GenotypingData<>(ploidyModel,readLikelihoods));

21
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
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@ -129,11 +129,22 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
public enum PCR_ERROR_MODEL {
/** no specialized PCR error model will be applied; if base insertion/deletion qualities are present they will be used */
NONE,
NONE(null),
/** a most aggressive model will be applied that sacrifices true positives in order to remove more false positives */
HOSTILE(1.0),
/** a more aggressive model will be applied that sacrifices true positives in order to remove more false positives */
AGGRESSIVE,
AGGRESSIVE(2.0),
/** a less aggressive model will be applied that tries to maintain a high true positive rate at the expense of allowing more false positives */
CONSERVATIVE
CONSERVATIVE(3.0);
private final Double rateFactor;
/** rate factor is applied to the PCR error model. Can be null to imply no correction */
PCR_ERROR_MODEL(Double rateFactor) {
this.rateFactor = rateFactor;
}
private Double getRateFactor() { return rateFactor; }
private boolean hasRateFactor() { return rateFactor != null; }
}
private final PCR_ERROR_MODEL pcrErrorModel;
@ -421,14 +432,14 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
private final RepeatCovariate repeatCovariate = new RepeatLengthCovariate();
private void initializePCRErrorModel() {
if ( pcrErrorModel == PCR_ERROR_MODEL.NONE )
if ( pcrErrorModel == PCR_ERROR_MODEL.NONE || !pcrErrorModel.hasRateFactor() )
return;
repeatCovariate.initialize(MAX_STR_UNIT_LENGTH, MAX_REPEAT_LENGTH);
pcrIndelErrorModelCache = new byte[MAX_REPEAT_LENGTH + 1];
final double rateFactor = pcrErrorModel == PCR_ERROR_MODEL.AGGRESSIVE ? 2.0 : 3.0;
final double rateFactor = pcrErrorModel.getRateFactor();
for( int iii = 0; iii <= MAX_REPEAT_LENGTH; iii++ )
pcrIndelErrorModelCache[iii] = getErrorModelAdjustedQual(iii, rateFactor);