diff --git a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java new file mode 100755 index 000000000..e224a9c57 --- /dev/null +++ b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java @@ -0,0 +1,195 @@ +/* + * Copyright (c) 2010. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.gatk.downsampling; + +import net.sf.samtools.SAMReadGroupRecord; +import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.pileup.*; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.variantcontext.Allele; + +import java.io.PrintStream; +import java.util.*; + +public class AlleleBiasedDownsamplingUtils { + + private static final ArrayList[] alleleStratifiedElements = new ArrayList[4]; + static { + for ( int i = 0; i < 4; i++ ) + alleleStratifiedElements[i] = new ArrayList(); + } + + /** + * Computes an allele biased version of the given pileup + * + * @param pileup the original pileup + * @param downsamplingFraction the fraction of total reads to remove per allele + * @param log logging output + * @return allele biased pileup + */ + public synchronized static ReadBackedPileup createAlleleBiasedBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { + // special case removal of all or no reads + if ( downsamplingFraction <= 0.0 ) + return pileup; + if ( downsamplingFraction >= 1.0 ) + return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList()); + + // start by stratifying the reads by the alleles they represent at this position + for( final PileupElement pe : pileup ) { + final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase()); + if ( baseIndex != -1 ) + alleleStratifiedElements[baseIndex].add(pe); + } + + // Down-sample *each* allele by the contamination fraction applied to the entire pileup. + // Unfortunately, we need to maintain the original pileup ordering of reads or FragmentUtils will complain later. + int numReadsToRemove = (int)(pileup.getNumberOfElements() * downsamplingFraction); // floor + final TreeSet elementsToKeep = new TreeSet(new Comparator() { + @Override + public int compare(PileupElement element1, PileupElement element2) { + final int difference = element1.getRead().getAlignmentStart() - element2.getRead().getAlignmentStart(); + return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName()); + } + }); + + for ( int i = 0; i < 4; i++ ) { + final ArrayList alleleList = alleleStratifiedElements[i]; + if ( alleleList.size() <= numReadsToRemove ) + logAllElements(alleleList, log); + else + elementsToKeep.addAll(downsampleElements(alleleList, numReadsToRemove, log)); + } + + // clean up pointers so memory can be garbage collected if needed + for ( int i = 0; i < 4; i++ ) + alleleStratifiedElements[i].clear(); + + return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList(elementsToKeep)); + } + + /** + * Performs allele biased down-sampling on a pileup and computes the list of elements to keep + * + * @param elements original list of records + * @param numElementsToRemove the number of records to remove + * @param log logging output + * @return the list of pileup elements TO KEEP + */ + private static List downsampleElements(final ArrayList elements, final int numElementsToRemove, final PrintStream log) { + final int pileupSize = elements.size(); + final BitSet itemsToRemove = new BitSet(pileupSize); + for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) { + itemsToRemove.set(selectedIndex); + } + + ArrayList elementsToKeep = new ArrayList(pileupSize - numElementsToRemove); + for ( int i = 0; i < pileupSize; i++ ) { + if ( itemsToRemove.get(i) ) + logRead(elements.get(i).getRead(), log); + else + elementsToKeep.add(elements.get(i)); + } + + return elementsToKeep; + } + + /** + * Computes reads to remove based on an allele biased down-sampling + * + * @param alleleReadMap original list of records per allele + * @param downsamplingFraction the fraction of total reads to remove per allele + * @param log logging output + * @return list of reads TO REMOVE from allele biased down-sampling + */ + public static List selectAlleleBiasedReads(final Map> alleleReadMap, final double downsamplingFraction, final PrintStream log) { + int totalReads = 0; + for ( final List reads : alleleReadMap.values() ) + totalReads += reads.size(); + + // Down-sample *each* allele by the contamination fraction applied to the entire pileup. + int numReadsToRemove = (int)(totalReads * downsamplingFraction); + final List readsToRemove = new ArrayList(numReadsToRemove * alleleReadMap.size()); + for ( final List reads : alleleReadMap.values() ) { + if ( reads.size() <= numReadsToRemove ) { + readsToRemove.addAll(reads); + logAllReads(reads, log); + } else { + readsToRemove.addAll(downsampleReads(reads, numReadsToRemove, log)); + } + } + + return readsToRemove; + } + + /** + * Performs allele biased down-sampling on a pileup and computes the list of elements to remove + * + * @param reads original list of records + * @param numElementsToRemove the number of records to remove + * @param log logging output + * @return the list of pileup elements TO REMOVE + */ + private static List downsampleReads(final List reads, final int numElementsToRemove, final PrintStream log) { + final int pileupSize = reads.size(); + final BitSet itemsToRemove = new BitSet(pileupSize); + for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) { + itemsToRemove.set(selectedIndex); + } + + ArrayList readsToRemove = new ArrayList(pileupSize - numElementsToRemove); + for ( int i = 0; i < pileupSize; i++ ) { + if ( itemsToRemove.get(i) ) { + final GATKSAMRecord read = reads.get(i); + readsToRemove.add(read); + logRead(read, log); + } + } + + return readsToRemove; + } + + private static void logAllElements(final List elements, final PrintStream log) { + if ( log != null ) { + for ( final PileupElement p : elements ) + logRead(p.getRead(), log); + } + } + + private static void logAllReads(final List reads, final PrintStream log) { + if ( log != null ) { + for ( final GATKSAMRecord read : reads ) + logRead(read, log); + } + } + + private static void logRead(final SAMRecord read, final PrintStream log) { + if ( log != null ) { + final SAMReadGroupRecord readGroup = read.getReadGroup(); + log.println(String.format("%s\t%s\t%s\t%s", read.getReadName(), readGroup.getSample(), readGroup.getLibrary(), readGroup.getPlatformUnit())); + } + } +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java index b89f68e24..be8357679 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java @@ -28,26 +28,22 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource; -import org.broadinstitute.sting.utils.collections.NestedIntegerArray; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.recalibration.ReadCovariates; -import org.broadinstitute.sting.utils.recalibration.RecalDatum; import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.threading.ThreadLocalArray; public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine implements ProtectedPackageSource { - // optimizations: don't reallocate an array each time - private byte[] tempQualArray; - private boolean[] tempErrorArray; - private double[] tempFractionalErrorArray; + // optimization: only allocate temp arrays once per thread + private final ThreadLocal threadLocalTempQualArray = new ThreadLocalArray(EventType.values().length, byte.class); + private final ThreadLocal threadLocalTempErrorArray = new ThreadLocalArray(EventType.values().length, boolean.class); + private final ThreadLocal threadLocalTempFractionalErrorArray = new ThreadLocalArray(EventType.values().length, double.class); public void initialize(final Covariate[] covariates, final RecalibrationTables recalibrationTables) { super.initialize(covariates, recalibrationTables); - tempQualArray = new byte[EventType.values().length]; - tempErrorArray = new boolean[EventType.values().length]; - tempFractionalErrorArray = new double[EventType.values().length]; } /** @@ -60,10 +56,13 @@ public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine imp * @param refBase The reference base at this locus */ @Override - public synchronized void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase) { + public void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase) { final int offset = pileupElement.getOffset(); final ReadCovariates readCovariates = covariateKeySetFrom(pileupElement.getRead()); + byte[] tempQualArray = threadLocalTempQualArray.get(); + boolean[] tempErrorArray = threadLocalTempErrorArray.get(); + tempQualArray[EventType.BASE_SUBSTITUTION.index] = pileupElement.getQual(); tempErrorArray[EventType.BASE_SUBSTITUTION.index] = !BaseUtils.basesAreEqual(pileupElement.getBase(), refBase); tempQualArray[EventType.BASE_INSERTION.index] = pileupElement.getBaseInsertionQual(); @@ -77,40 +76,29 @@ public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine imp final byte qual = tempQualArray[eventIndex]; final boolean isError = tempErrorArray[eventIndex]; - final NestedIntegerArray rgRecalTable = recalibrationTables.getReadGroupTable(); - final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex); - final RecalDatum rgThisDatum = createDatumObject(qual, isError); - if (rgPreviousDatum == null) // key doesn't exist yet in the map so make a new bucket and add it - rgRecalTable.put(rgThisDatum, keys[0], eventIndex); - else - rgPreviousDatum.combine(rgThisDatum); + // TODO: should this really be combine rather than increment? + combineDatumOrPutIfNecessary(recalibrationTables.getReadGroupTable(), qual, isError, keys[0], eventIndex); - final NestedIntegerArray qualRecalTable = recalibrationTables.getQualityScoreTable(); - final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex); - if (qualPreviousDatum == null) - qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex); - else - qualPreviousDatum.increment(isError); + incrementDatumOrPutIfNecessary(recalibrationTables.getQualityScoreTable(), qual, isError, keys[0], keys[1], eventIndex); for (int i = 2; i < covariates.length; i++) { if (keys[i] < 0) continue; - final NestedIntegerArray covRecalTable = recalibrationTables.getTable(i); - final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex); - if (covPreviousDatum == null) - covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex); - else - covPreviousDatum.increment(isError); + + incrementDatumOrPutIfNecessary(recalibrationTables.getTable(i), qual, isError, keys[0], keys[1], keys[i], eventIndex); } } } @Override - public synchronized void updateDataForRead(final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) { + public void updateDataForRead(final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) { for( int offset = 0; offset < read.getReadBases().length; offset++ ) { if( !skip[offset] ) { final ReadCovariates readCovariates = covariateKeySetFrom(read); + byte[] tempQualArray = threadLocalTempQualArray.get(); + double[] tempFractionalErrorArray = threadLocalTempFractionalErrorArray.get(); + tempQualArray[EventType.BASE_SUBSTITUTION.index] = read.getBaseQualities()[offset]; tempFractionalErrorArray[EventType.BASE_SUBSTITUTION.index] = snpErrors[offset]; tempQualArray[EventType.BASE_INSERTION.index] = read.getBaseInsertionQualities()[offset]; @@ -124,30 +112,15 @@ public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine imp final byte qual = tempQualArray[eventIndex]; final double isError = tempFractionalErrorArray[eventIndex]; - final NestedIntegerArray rgRecalTable = recalibrationTables.getReadGroupTable(); - final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex); - final RecalDatum rgThisDatum = createDatumObject(qual, isError); - if (rgPreviousDatum == null) // key doesn't exist yet in the map so make a new bucket and add it - rgRecalTable.put(rgThisDatum, keys[0], eventIndex); - else - rgPreviousDatum.combine(rgThisDatum); + combineDatumOrPutIfNecessary(recalibrationTables.getReadGroupTable(), qual, isError, keys[0], eventIndex); - final NestedIntegerArray qualRecalTable = recalibrationTables.getQualityScoreTable(); - final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex); - if (qualPreviousDatum == null) - qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex); - else - qualPreviousDatum.increment(1.0, isError); + incrementDatumOrPutIfNecessary(recalibrationTables.getQualityScoreTable(), qual, isError, keys[0], keys[1], eventIndex); for (int i = 2; i < covariates.length; i++) { if (keys[i] < 0) continue; - final NestedIntegerArray covRecalTable = recalibrationTables.getTable(i); - final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex); - if (covPreviousDatum == null) - covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex); - else - covPreviousDatum.increment(1.0, isError); + + incrementDatumOrPutIfNecessary(recalibrationTables.getTable(i), qual, isError, keys[0], keys[1], keys[i], eventIndex); } } } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java index 8042c15d8..fc6d23382 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java @@ -1,11 +1,11 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import com.google.java.contract.Requires; -import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variantcontext.Allele; @@ -60,7 +60,7 @@ public class ErrorModel { boolean hasCalledAlleles = false; - final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap(); + final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap(); if (refSampleVC != null) { for (Allele allele : refSampleVC.getAlleles()) { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java index 2522fc16e..f6ad445c7 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java @@ -195,7 +195,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G final List allAllelesToUse, final boolean useBAQedPileup, final GenomeLocParser locParser, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { HashMap perLaneErrorModels = getPerLaneErrorModels(tracker, ref, contexts); if (perLaneErrorModels == null && UAC.referenceSampleName != null) @@ -231,7 +231,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G ReadBackedPileup pileup = AlignmentContextUtils.stratify(sample.getValue(), contextType).getBasePileup(); if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){ // no likelihoods have been computed for this sample at this site - perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap()); + perReadAlleleLikelihoodMap.put(sample.getKey(), org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap()); } // create the GenotypeLikelihoods object @@ -333,7 +333,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G final boolean useBQAedPileup, final ReferenceContext ref, final boolean ignoreLaneInformation, - final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap); + final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap); protected abstract List getInitialAllelesToUse(final RefMetaDataTracker tracker, final ReferenceContext ref, diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java index afbd49a08..4bcaa5ff9 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java @@ -27,7 +27,7 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype double[][] readHaplotypeLikelihoods; final byte refBase; - final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap; + final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap; public GeneralPloidyIndelGenotypeLikelihoods(final List alleles, final double[] logLikelihoods, @@ -37,7 +37,7 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype final PairHMMIndelErrorModel pairModel, final LinkedHashMap haplotypeMap, final ReferenceContext referenceContext, - final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap) { + final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap) { super(alleles, logLikelihoods, ploidy, perLaneErrorModels, ignoreLaneInformation); this.pairModel = pairModel; this.haplotypeMap = haplotypeMap; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java index f09a1ea3e..eb4cf1839 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java @@ -74,7 +74,7 @@ public class GeneralPloidyIndelGenotypeLikelihoodsCalculationModel extends Gener final boolean useBQAedPileup, final ReferenceContext ref, final boolean ignoreLaneInformation, - final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){ + final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){ return new GeneralPloidyIndelGenotypeLikelihoods(alleles, logLikelihoods, ploidy,perLaneErrorModels,ignoreLaneInformation, pairModel, haplotypeMap, ref, perReadAlleleLikelihoodMap); } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java index 4376ec601..9f2fdc096 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java @@ -50,7 +50,7 @@ public class GeneralPloidySNPGenotypeLikelihoodsCalculationModel extends General final boolean useBQAedPileup, final ReferenceContext ref, final boolean ignoreLaneInformation, - final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){ + final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){ return new GeneralPloidySNPGenotypeLikelihoods(alleles, null, UAC.samplePloidy, perLaneErrorModels, useBQAedPileup, UAC.IGNORE_LANE_INFO); } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java index 8738def50..d91df82e2 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java @@ -217,7 +217,7 @@ public class GenotypingEngine { } cleanUpSymbolicUnassembledEvents( haplotypes ); - if( activeAllelesToGenotype.isEmpty() && haplotypes.get(0).getSampleKeySet().size() >= 3 ) { // if not in GGA mode and have at least 3 samples try to create MNP and complex events by looking at LD structure + if( activeAllelesToGenotype.isEmpty() && haplotypes.get(0).getSampleKeySet().size() >= 10 ) { // if not in GGA mode and have at least 10 samples try to create MNP and complex events by looking at LD structure mergeConsecutiveEventsBasedOnLD( haplotypes, startPosKeySet, ref, refLoc ); } if( !activeAllelesToGenotype.isEmpty() ) { // we are in GGA mode! diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index a08614deb..5aba23faa 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -51,6 +51,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.fragments.FragmentCollection; import org.broadinstitute.sting.utils.fragments.FragmentUtils; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pairhmm.PairHMM; import org.broadinstitute.sting.utils.pileup.PileupElement; @@ -424,7 +425,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem : genotypingEngine.assignGenotypeLikelihoodsAndCallIndependentEvents( UG_engine, bestHaplotypes, fullReferenceWithPadding, getPaddedLoc(activeRegion), activeRegion.getLocation(), getToolkit().getGenomeLocParser(), activeAllelesToGenotype ) ) ) { if( DEBUG ) { System.out.println(callResult.getFirst().toStringWithoutGenotypes()); } - final Map stratifiedReadMap = LikelihoodCalculationEngine.partitionReadsBasedOnLikelihoods( getToolkit().getGenomeLocParser(), perSampleReadList, perSampleFilteredReadList, callResult ); + final Map stratifiedReadMap = LikelihoodCalculationEngine.partitionReadsBasedOnLikelihoods( getToolkit().getGenomeLocParser(), perSampleReadList, perSampleFilteredReadList, callResult, UG_engine.getUAC().CONTAMINATION_FRACTION, UG_engine.getUAC().contaminationLog ); final VariantContext annotatedCall = annotationEngine.annotateContext(stratifiedReadMap, callResult.getFirst()); final Map myAttributes = new LinkedHashMap(annotatedCall.getAttributes()); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java index 62554c4ab..a0924623b 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import java.io.PrintStream; import java.util.*; public class LikelihoodCalculationEngine { @@ -139,7 +140,7 @@ public class LikelihoodCalculationEngine { } private static int computeFirstDifferingPosition( final byte[] b1, final byte[] b2 ) { - for( int iii = 0; iii < b1.length && iii < b2.length; iii++ ){ + for( int iii = 0; iii < b1.length && iii < b2.length; iii++ ) { if( b1[iii] != b2[iii] ) { return iii; } @@ -346,11 +347,13 @@ public class LikelihoodCalculationEngine { public static Map partitionReadsBasedOnLikelihoods( final GenomeLocParser parser, final HashMap> perSampleReadList, final HashMap> perSampleFilteredReadList, - final Pair>> call) { + final Pair>> call, + final double downsamplingFraction, + final PrintStream downsamplingLog ) { final Map returnMap = new HashMap(); final GenomeLoc callLoc = parser.createGenomeLoc(call.getFirst()); for( final Map.Entry> sample : perSampleReadList.entrySet() ) { - final PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap(); + final PerReadAlleleLikelihoodMap likelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap(); final ArrayList readsForThisSample = sample.getValue(); for( int iii = 0; iii < readsForThisSample.size(); iii++ ) { @@ -370,6 +373,9 @@ public class LikelihoodCalculationEngine { } } + // down-sample before adding filtered reads + likelihoodMap.performPerAlleleDownsampling(downsamplingFraction, downsamplingLog); + // add all filtered reads to the NO_CALL list because they weren't given any likelihoods for( final GATKSAMRecord read : perSampleFilteredReadList.get(sample.getKey()) ) { // only count the read if it overlaps the event, otherwise it is not added to the output read list at all diff --git a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java new file mode 100644 index 000000000..d6cddcf84 --- /dev/null +++ b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java @@ -0,0 +1,68 @@ +/* + * Copyright (c) 2011 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ +package org.broadinstitute.sting.utils.genotyper; + + +import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils; +import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.variantcontext.Allele; + +import java.io.PrintStream; +import java.util.*; + +public class AdvancedPerReadAlleleLikelihoodMap extends StandardPerReadAlleleLikelihoodMap implements ProtectedPackageSource { + + public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { + return AlleleBiasedDownsamplingUtils.createAlleleBiasedBasePileup(pileup, downsamplingFraction, log); + } + + public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) { + // special case removal of all or no reads + if ( downsamplingFraction <= 0.0 ) + return; + if ( downsamplingFraction >= 1.0 ) { + likelihoodReadMap.clear(); + return; + } + + // start by stratifying the reads by the alleles they represent at this position + final Map> alleleReadMap = new HashMap>(alleles.size()); + for ( Allele allele : alleles ) + alleleReadMap.put(allele, new ArrayList()); + + for ( Map.Entry> entry : likelihoodReadMap.entrySet() ) { + final Allele bestAllele = getMostLikelyAllele(entry.getValue()); + if ( bestAllele != Allele.NO_CALL ) + alleleReadMap.get(bestAllele).add(entry.getKey()); + } + + // compute the reads to remove and actually remove them + final List readsToRemove = AlleleBiasedDownsamplingUtils.selectAlleleBiasedReads(alleleReadMap, downsamplingFraction, log); + for ( final GATKSAMRecord read : readsToRemove ) + likelihoodReadMap.remove(read); + } +} diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java index 26ee78484..a50219f48 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java @@ -5,7 +5,9 @@ import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; +import java.util.ArrayList; import java.util.Arrays; +import java.util.List; /** * @author ebanks @@ -73,11 +75,6 @@ public class BQSRIntegrationTest extends WalkerTest { params.getCommandLine(), Arrays.asList(params.md5)); executeTest("testBQSR-"+params.args, spec).getFirst(); - - WalkerTestSpec specNT2 = new WalkerTestSpec( - params.getCommandLine() + " -nt 2", - Arrays.asList(params.md5)); - executeTest("testBQSR-nt2-"+params.args, specNT2).getFirst(); } @Test @@ -123,20 +120,26 @@ public class BQSRIntegrationTest extends WalkerTest { @DataProvider(name = "PRTest") public Object[][] createPRTestData() { - return new Object[][]{ - {new PRTest("", "ab2f209ab98ad3432e208cbd524a4c4a")}, - {new PRTest(" -qq -1", "5226c06237b213b9e9b25a32ed92d09a")}, - {new PRTest(" -qq 6", "b592a5c62b952a012e18adb898ea9c33")}, - {new PRTest(" -DIQ", "8977bea0c57b808e65e9505eb648cdf7")} - }; + List tests = new ArrayList(); + + tests.add(new Object[]{1, new PRTest(" -qq -1", "a1d87da5dcbde35170d6ba6bc3ee2812")}); + tests.add(new Object[]{1, new PRTest(" -qq 6", "a0fecae6d0e5ab9917862fa306186d10")}); + tests.add(new Object[]{1, new PRTest(" -DIQ", "8977bea0c57b808e65e9505eb648cdf7")}); + + for ( final int nct : Arrays.asList(1, 2, 4) ) { + tests.add(new Object[]{nct, new PRTest("", "d1bbb4ce6aa93e866f106f8b11d888ed")}); + } + + return tests.toArray(new Object[][]{}); } @Test(dataProvider = "PRTest") - public void testPR(PRTest params) { + public void testPR(final int nct, PRTest params) { WalkerTestSpec spec = new WalkerTestSpec( "-T PrintReads" + " -R " + hg18Reference + " -I " + privateTestDir + "HiSeq.1mb.1RG.bam" + + " -nct " + nct + " -BQSR " + privateTestDir + "HiSeq.20mb.1RG.table" + params.args + " -o %s", diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 1d4fad19e..71f03ea00 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -21,7 +21,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "ee866a8694a6f6c77242041275350ab9"); + HCTest(CEUTRIO_BAM, "", "1d826f852ec1457efbfa7ee828c5783a"); } @Test @@ -42,7 +42,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSampleComplex() { - HCTestComplexVariants(CEUTRIO_BAM, "", "30598abeeb0b0ae5816ffdbf0c4044fd"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "966d338f423c86a390d685aa6336ec69"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { @@ -94,6 +94,4 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { Arrays.asList("79af83432dc4a1768b3ebffffc4d2b8f")); executeTest("HC calling on a ReducedRead BAM", spec); } - - } diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java index aa3a1e6ac..2f6d9d16f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java @@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.File; +import java.io.PrintStream; /** * Created with IntelliJ IDEA. @@ -63,26 +64,23 @@ public class StandardCallerArgumentCollection { public int MAX_ALTERNATE_ALLELES = 6; /** - * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES), - * then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it - * scales exponentially based on the number of alternate alleles. Unless there is a good reason to change the default value, we highly recommend - * that you not play around with this parameter. - * - * This argument has been retired in GATK 2.2. Please specify just maxAltAlleles from now on + * Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus. */ - @Deprecated - @Hidden - @Argument(fullName = "max_alternate_alleles_for_indels", shortName = "maxAltAllelesForIndels", doc = "This argument has been retired in GATK 2.2. Please specify just maxAltAlleles from now on, which will apply to any variant, regardless of type", required = false) - public int MAX_ALTERNATE_ALLELES_FOR_INDELS = -1; + @Advanced + @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false) + public AFCalcFactory.Calculation AFmodel = AFCalcFactory.Calculation.getDefaultModel(); /** * If this fraction is greater is than zero, the caller will aggressively attempt to remove contamination through biased down-sampling of reads. * Basically, it will ignore the contamination fraction of reads for each alternate allele. So if the pileup contains N total bases, then we * will try to remove (N * contamination fraction) bases for each alternate allele. */ - @Hidden @Argument(fullName = "contamination_percentage_to_filter", shortName = "contamination", doc = "Fraction of contamination in sequencing data (for all samples) to aggressively remove", required = false) - public double CONTAMINATION_PERCENTAGE = 0.0; + public double CONTAMINATION_FRACTION = 0.0; + + @Hidden + @Argument(fullName = "logRemovedReadsFromContaminationFiltering", shortName="contaminationLog", required=false) + public PrintStream contaminationLog = null; @Hidden @Argument(shortName = "logExactCalls", doc="x", required=false) @@ -96,19 +94,12 @@ public class StandardCallerArgumentCollection { this.GenotypingMode = SCAC.GenotypingMode; this.heterozygosity = SCAC.heterozygosity; this.MAX_ALTERNATE_ALLELES = SCAC.MAX_ALTERNATE_ALLELES; - this.MAX_ALTERNATE_ALLELES_FOR_INDELS = SCAC.MAX_ALTERNATE_ALLELES_FOR_INDELS; this.OutputMode = SCAC.OutputMode; this.STANDARD_CONFIDENCE_FOR_CALLING = SCAC.STANDARD_CONFIDENCE_FOR_CALLING; this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING; - this.CONTAMINATION_PERCENTAGE = SCAC.CONTAMINATION_PERCENTAGE; + this.CONTAMINATION_FRACTION = SCAC.CONTAMINATION_FRACTION; + this.contaminationLog = SCAC.contaminationLog; this.exactCallsLog = SCAC.exactCallsLog; this.AFmodel = SCAC.AFmodel; } - - /** - * Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus. - */ - @Advanced - @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false) - public AFCalcFactory.Calculation AFmodel = AFCalcFactory.Calculation.getDefaultModel(); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java index a68f0df21..18bdb02ed 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java index 1e1f65333..4d79c4112 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java @@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java index 3cbca4f52..aef3e49cf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java @@ -36,7 +36,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java index 577b1cfdc..e59fc827d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java @@ -1,14 +1,11 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.variantcontext.Allele; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java index 4ae1a0bba..0c78c0204 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java @@ -34,13 +34,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java index c74f98ca3..1dff4d1a3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java index 1cc88fc24..c9481f244 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java @@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java index d7790969e..89a239e54 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java @@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index ec0393cdc..bdf7baec9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java index 3fe5c5837..07391c78c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java @@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index 6487eac50..ca7180510 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -32,8 +32,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.MathUtils; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java index 06fa04526..0340f457c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java @@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java index 5891cbc69..037b357ae 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java @@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java index 9a4de3c36..dd058b469 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java @@ -8,12 +8,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java index 5f405cb46..c67d829c2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java @@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.IndelUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java index 4be601bc8..c9a4d0ee6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java @@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java index 85f61c91c..c9d5ca261 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java @@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MendelianViolation; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java index 787c9b29b..82596a501 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java @@ -1,14 +1,11 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.variantcontext.Allele; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java index 74f9c0d0c..364bbdbb9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java @@ -7,14 +7,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Arrays; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java index 44657a7e7..afb4ceb60 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java index 21ee66ea2..5f9f3416d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java @@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java index 8e4edaf0e..3e6aa62a2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java @@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java index a48d4a678..d75947879 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java @@ -7,11 +7,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java index 680478da0..474b6b150 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java @@ -7,16 +7,14 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java index 7c7391812..0df7aff71 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java @@ -7,15 +7,13 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MannWhitneyU; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index de0ce2ce2..d01233bb2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java @@ -5,7 +5,7 @@ import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java index abe55de5a..33e895187 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java index f0bd7ecd9..b3b0be153 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java @@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java index f6bb4e747..8e1140af1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java @@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java index 3d62f2d96..c72ba1c5f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java index 43ef188a8..57b50c6e2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java @@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java index c3e98c20f..be7288a7e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java @@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index eae13e1b5..ee4f77752 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java index 9c5710872..03fcba760 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java @@ -1,9 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java index 6c55c1c00..6970908b5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java index 738be9883..5b2dc310d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.variantcontext.VariantContext; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 2c7a12a36..245c8e3e8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -109,7 +109,7 @@ import java.util.ArrayList; @ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class}) // only look at covered loci, not every loci of the reference file @Requires({DataSource.READS, DataSource.REFERENCE}) // filter out all reads with zero or unavailable mapping quality @PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta -public class BaseRecalibrator extends LocusWalker implements TreeReducible, NanoSchedulable { +public class BaseRecalibrator extends LocusWalker { @ArgumentCollection private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates @@ -277,11 +277,6 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed return sum; } - public Long treeReduce(Long sum1, Long sum2) { - sum1 += sum2; - return sum1; - } - @Override public void onTraversalDone(Long result) { logger.info("Calculating quantized quality scores..."); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java index 4fe9c5323..1f7fbbf42 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java @@ -55,7 +55,7 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP * @param refBase The reference base at this locus */ @Override - public synchronized void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase) { + public void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase) { final int offset = pileupElement.getOffset(); final ReadCovariates readCovariates = covariateKeySetFrom(pileupElement.getRead()); @@ -65,35 +65,21 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP final int[] keys = readCovariates.getKeySet(offset, EventType.BASE_SUBSTITUTION); final int eventIndex = EventType.BASE_SUBSTITUTION.index; - final NestedIntegerArray rgRecalTable = recalibrationTables.getReadGroupTable(); - final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex); - final RecalDatum rgThisDatum = createDatumObject(qual, isError); - if (rgPreviousDatum == null) // key doesn't exist yet in the map so make a new bucket and add it - rgRecalTable.put(rgThisDatum, keys[0], eventIndex); - else - rgPreviousDatum.combine(rgThisDatum); + // TODO: should this really be combine rather than increment? + combineDatumOrPutIfNecessary(recalibrationTables.getReadGroupTable(), qual, isError, keys[0], eventIndex); - final NestedIntegerArray qualRecalTable = recalibrationTables.getQualityScoreTable(); - final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex); - if (qualPreviousDatum == null) - qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex); - else - qualPreviousDatum.increment(isError); + incrementDatumOrPutIfNecessary(recalibrationTables.getQualityScoreTable(), qual, isError, keys[0], keys[1], eventIndex); for (int i = 2; i < covariates.length; i++) { if (keys[i] < 0) continue; - final NestedIntegerArray covRecalTable = recalibrationTables.getTable(i); - final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex); - if (covPreviousDatum == null) - covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex); - else - covPreviousDatum.increment(isError); + + incrementDatumOrPutIfNecessary(recalibrationTables.getTable(i), qual, isError, keys[0], keys[1], keys[i], eventIndex); } } @Override - public synchronized void updateDataForRead( final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) { + public void updateDataForRead( final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) { throw new UnsupportedOperationException("Delocalized BQSR is not available in the GATK-lite version"); } @@ -121,4 +107,133 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) { return (ReadCovariates) read.getTemporaryAttribute(BaseRecalibrator.COVARS_ATTRIBUTE); } + + /** + * Increments the RecalDatum at the specified position in the specified table, or put a new item there + * if there isn't already one. + * + * Does this in a thread-safe way WITHOUT being synchronized: relies on the behavior of NestedIntegerArray.put() + * to return false if another thread inserts a new item at our position in the middle of our put operation. + * + * @param table the table that holds/will hold our item + * @param qual qual for this event + * @param isError error status for this event + * @param keys location in table of our item + */ + protected void incrementDatumOrPutIfNecessary( final NestedIntegerArray table, final byte qual, final boolean isError, final int... keys ) { + final RecalDatum existingDatum = table.get(keys); + + // There are three cases here: + // + // 1. The original get succeeded (existingDatum != null) because there already was an item in this position. + // In this case we can just increment the existing item. + // + // 2. The original get failed (existingDatum == null), and we successfully put a new item in this position + // and are done. + // + // 3. The original get failed (existingDatum == null), AND the put fails because another thread comes along + // in the interim and puts an item in this position. In this case we need to do another get after the + // failed put to get the item the other thread put here and increment it. + if ( existingDatum == null ) { + // No existing item, try to put a new one + if ( ! table.put(createDatumObject(qual, isError), keys) ) { + // Failed to put a new item because another thread came along and put an item here first. + // Get the newly-put item and increment it (item is guaranteed to exist at this point) + table.get(keys).increment(isError); + } + } + else { + // Easy case: already an item here, so increment it + existingDatum.increment(isError); + } + } + + /** + * Increments the RecalDatum at the specified position in the specified table, or put a new item there + * if there isn't already one. + * + * Does this in a thread-safe way WITHOUT being synchronized: relies on the behavior of NestedIntegerArray.put() + * to return false if another thread inserts a new item at our position in the middle of our put operation. + * + * @param table the table that holds/will hold our item + * @param qual qual for this event + * @param isError error value for this event + * @param keys location in table of our item + */ + protected void incrementDatumOrPutIfNecessary( final NestedIntegerArray table, final byte qual, final double isError, final int... keys ) { + final RecalDatum existingDatum = table.get(keys); + + if ( existingDatum == null ) { + // No existing item, try to put a new one + if ( ! table.put(createDatumObject(qual, isError), keys) ) { + // Failed to put a new item because another thread came along and put an item here first. + // Get the newly-put item and increment it (item is guaranteed to exist at this point) + table.get(keys).increment(1.0, isError); + } + } + else { + // Easy case: already an item here, so increment it + existingDatum.increment(1.0, isError); + } + } + + /** + * Combines the RecalDatum at the specified position in the specified table with a new RecalDatum, or put a + * new item there if there isn't already one. + * + * Does this in a thread-safe way WITHOUT being synchronized: relies on the behavior of NestedIntegerArray.put() + * to return false if another thread inserts a new item at our position in the middle of our put operation. + * + * @param table the table that holds/will hold our item + * @param qual qual for this event + * @param isError error status for this event + * @param keys location in table of our item + */ + protected void combineDatumOrPutIfNecessary( final NestedIntegerArray table, final byte qual, final boolean isError, final int... keys ) { + final RecalDatum existingDatum = table.get(keys); + final RecalDatum newDatum = createDatumObject(qual, isError); + + if ( existingDatum == null ) { + // No existing item, try to put a new one + if ( ! table.put(newDatum, keys) ) { + // Failed to put a new item because another thread came along and put an item here first. + // Get the newly-put item and combine it with our item (item is guaranteed to exist at this point) + table.get(keys).combine(newDatum); + } + } + else { + // Easy case: already an item here, so combine it with our item + existingDatum.combine(newDatum); + } + } + + /** + * Combines the RecalDatum at the specified position in the specified table with a new RecalDatum, or put a + * new item there if there isn't already one. + * + * Does this in a thread-safe way WITHOUT being synchronized: relies on the behavior of NestedIntegerArray.put() + * to return false if another thread inserts a new item at our position in the middle of our put operation. + * + * @param table the table that holds/will hold our item + * @param qual qual for this event + * @param isError error value for this event + * @param keys location in table of our item + */ + protected void combineDatumOrPutIfNecessary( final NestedIntegerArray table, final byte qual, final double isError, final int... keys ) { + final RecalDatum existingDatum = table.get(keys); + final RecalDatum newDatum = createDatumObject(qual, isError); + + if ( existingDatum == null ) { + // No existing item, try to put a new one + if ( ! table.put(newDatum, keys) ) { + // Failed to put a new item because another thread came along and put an item here first. + // Get the newly-put item and combine it with our item (item is guaranteed to exist at this point) + table.get(keys).combine(newDatum); + } + } + else { + // Easy case: already an item here, so combine it with our item + existingDatum.combine(newDatum); + } + } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index 77da35c41..ae9b01f2d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -104,7 +104,7 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable { final List allAllelesToUse, final boolean useBAQedPileup, final GenomeLocParser locParser, - final Map perReadAlleleLikelihoodMap); + final Map perReadAlleleLikelihoodMap); protected int getFilteredDepth(ReadBackedPileup pileup) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 1761f9cec..0d9f443e2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Haplotype; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variantcontext.*; @@ -81,7 +82,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood final List allAllelesToUse, final boolean useBAQedPileup, final GenomeLocParser locParser, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { GenomeLoc loc = ref.getLocus(); // if (!ref.getLocus().equals(lastSiteVisited)) { @@ -118,12 +119,12 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){ // no likelihoods have been computed for this sample at this site - perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap()); + perReadAlleleLikelihoodMap.put(sample.getKey(), PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap()); } final ReadBackedPileup pileup = context.getBasePileup(); if (pileup != null) { final GenotypeBuilder b = new GenotypeBuilder(sample.getKey()); - final double[] genotypeLikelihoods = pairModel.computeDiploidReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, perReadAlleleLikelihoodMap.get(sample.getKey())); + final double[] genotypeLikelihoods = pairModel.computeDiploidReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, perReadAlleleLikelihoodMap.get(sample.getKey()), UAC.CONTAMINATION_FRACTION, UAC.contaminationLog); b.PL(genotypeLikelihoods); b.DP(getFilteredDepth(pileup)); genotypes.add(b.make()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index d053e13a8..791cdc325 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -36,6 +36,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; @@ -48,13 +49,13 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC private final boolean useAlleleFromVCF; private final double[] likelihoodSums = new double[4]; - private final ArrayList[] alleleStratifiedElements = new ArrayList[4]; + + private final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap; protected SNPGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) { super(UAC, logger); useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES; - for ( int i = 0; i < 4; i++ ) - alleleStratifiedElements[i] = new ArrayList(); + perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap(); } public VariantContext getLikelihoods(final RefMetaDataTracker tracker, @@ -64,9 +65,9 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC final List allAllelesToUse, final boolean useBAQedPileup, final GenomeLocParser locParser, - final Map perReadAlleleLikelihoodMap) { + final Map sampleLikelihoodMap) { - perReadAlleleLikelihoodMap.clear(); // not used in SNP model, sanity check to delete any older data + sampleLikelihoodMap.clear(); // not used in SNP model, sanity check to delete any older data final byte refBase = ref.getBase(); final int indexOfRefBase = BaseUtils.simpleBaseToBaseIndex(refBase); @@ -79,8 +80,8 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC ArrayList GLs = new ArrayList(contexts.size()); for ( Map.Entry sample : contexts.entrySet() ) { ReadBackedPileup pileup = AlignmentContextUtils.stratify(sample.getValue(), contextType).getBasePileup(); - if ( UAC.CONTAMINATION_PERCENTAGE > 0.0 ) - pileup = createDecontaminatedPileup(pileup, UAC.CONTAMINATION_PERCENTAGE); + if ( UAC.CONTAMINATION_FRACTION > 0.0 ) + pileup = perReadAlleleLikelihoodMap.createPerAlleleDownsampledBasePileup(pileup, UAC.CONTAMINATION_FRACTION, UAC.contaminationLog); if ( useBAQedPileup ) pileup = createBAQedPileup(pileup); @@ -203,42 +204,6 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC return allelesToUse; } - public ReadBackedPileup createDecontaminatedPileup(final ReadBackedPileup pileup, final double contaminationPercentage) { - // special case removal of all reads - if ( contaminationPercentage >= 1.0 ) - return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList()); - - // start by stratifying the reads by the alleles they represent at this position - for( final PileupElement pe : pileup ) { - final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase()); - if ( baseIndex != -1 ) - alleleStratifiedElements[baseIndex].add(pe); - } - - // Down-sample *each* allele by the contamination fraction applied to the entire pileup. - // Unfortunately, we need to maintain the original pileup ordering of reads or FragmentUtils will complain later. - int numReadsToRemove = (int)Math.ceil((double)pileup.getNumberOfElements() * contaminationPercentage); - final TreeSet elementsToKeep = new TreeSet(new Comparator() { - @Override - public int compare(PileupElement element1, PileupElement element2) { - final int difference = element1.getRead().getAlignmentStart() - element2.getRead().getAlignmentStart(); - return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName()); - } - }); - - for ( int i = 0; i < 4; i++ ) { - final ArrayList alleleList = alleleStratifiedElements[i]; - if ( alleleList.size() > numReadsToRemove ) - elementsToKeep.addAll(downsampleElements(alleleList, numReadsToRemove)); - } - - // clean up pointers so memory can be garbage collected if needed - for ( int i = 0; i < 4; i++ ) - alleleStratifiedElements[i].clear(); - - return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList(elementsToKeep)); - } - public ReadBackedPileup createBAQedPileup( final ReadBackedPileup pileup ) { final List BAQedElements = new ArrayList(); for( final PileupElement PE : pileup ) { @@ -257,22 +222,6 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC public byte getQual( final int offset ) { return BAQ.calcBAQFromTag(getRead(), offset, true); } } - private List downsampleElements(final ArrayList elements, final int numElementsToRemove) { - final int pileupSize = elements.size(); - final BitSet itemsToRemove = new BitSet(pileupSize); - for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) { - itemsToRemove.set(selectedIndex); - } - - ArrayList elementsToKeep = new ArrayList(pileupSize - numElementsToRemove); - for ( int i = 0; i < pileupSize; i++ ) { - if ( !itemsToRemove.get(i) ) - elementsToKeep.add(elements.get(i)); - } - - return elementsToKeep; - } - private static class SampleGenotypeData { public final String name; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 3116d3a7d..a17c2aa1a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -234,36 +234,21 @@ public class UnifiedGenotyper extends LocusWalker, Unif if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY || UAC.referenceSampleName != null || UAC.referenceSampleRod.isBound()) { - throw new UserException.NotSupportedInGATKLite("Usage of ploidy values different than 2 not supported in this GATK version"); + throw new UserException.NotSupportedInGATKLite("you cannot enable usage of ploidy values other than 2"); } + + if ( UAC.CONTAMINATION_FRACTION > 0.0 ) { + throw new UserException.NotSupportedInGATKLite("you cannot enable usage of contamination down-sampling"); + } + } + + if ( UAC.TREAT_ALL_READS_AS_SINGLE_POOL ) { + samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME); + } else { // get all of the unique sample names samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); - - } else { - // in full mode: check for consistency in ploidy/pool calling arguments - // check for correct calculation models -/* if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) { - // polyploidy requires POOL GL and AF calculation models to be specified right now - if (UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLSNP && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLINDEL - && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLBOTH) { - throw new UserException("Incorrect genotype calculation model chosen. Only [POOLSNP|POOLINDEL|POOLBOTH] supported with this walker if sample ploidy != 2"); - } - - if (UAC.AFmodel != AFCalc.Model.POOL) - throw new UserException("Incorrect AF Calculation model. Only POOL model supported if sample ploidy != 2"); - - } - */ - // get all of the unique sample names - if (UAC.TREAT_ALL_READS_AS_SINGLE_POOL) { - samples.clear(); - samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME); - } else { - samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); - if (UAC.referenceSampleName != null ) - samples.remove(UAC.referenceSampleName); - } - + if ( UAC.referenceSampleName != null ) + samples.remove(UAC.referenceSampleName); } // check for a bad max alleles value diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index a52b5dfe6..3c4a97ec1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -153,19 +153,19 @@ public class UnifiedGenotyperEngine { } - /** - * Compute full calls at a given locus. Entry point for engine calls from the UnifiedGenotyper. - * - * If allSamples != null, then the output variantCallContext is guarenteed to contain a genotype - * for every sample in allSamples. If it's null there's no such guarentee. Providing this - * argument is critical when the resulting calls will be written to a VCF file. - * - * @param tracker the meta data tracker - * @param refContext the reference base - * @param rawContext contextual information around the locus - * @param allSamples set of all sample names that we might call (i.e., those in the VCF header) - * @return the VariantCallContext object - */ + /** + * Compute full calls at a given locus. Entry point for engine calls from the UnifiedGenotyper. + * + * If allSamples != null, then the output variantCallContext is guarenteed to contain a genotype + * for every sample in allSamples. If it's null there's no such guarentee. Providing this + * argument is critical when the resulting calls will be written to a VCF file. + * + * @param tracker the meta data tracker + * @param refContext the reference base + * @param rawContext contextual information around the locus + * @param allSamples set of all sample names that we might call (i.e., those in the VCF header) + * @return the VariantCallContext object + */ public List calculateLikelihoodsAndGenotypes(final RefMetaDataTracker tracker, final ReferenceContext refContext, final AlignmentContext rawContext, @@ -174,7 +174,7 @@ public class UnifiedGenotyperEngine { final List models = getGLModelsToUse(tracker, refContext, rawContext); - final Map perReadAlleleLikelihoodMap = new HashMap(); + final Map perReadAlleleLikelihoodMap = new HashMap(); if ( models.isEmpty() ) { results.add(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, null, rawContext) : null); @@ -209,7 +209,7 @@ public class UnifiedGenotyperEngine { public VariantContext calculateLikelihoods(final RefMetaDataTracker tracker, final ReferenceContext refContext, final AlignmentContext rawContext, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { final List models = getGLModelsToUse(tracker, refContext, rawContext); if ( models.isEmpty() ) { return null; @@ -275,7 +275,7 @@ public class UnifiedGenotyperEngine { final List alternateAllelesToUse, final boolean useBAQedPileup, final GenotypeLikelihoodsCalculationModel.Model model, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { // initialize the data for this thread if that hasn't been done yet if ( glcm.get() == null ) { @@ -313,7 +313,7 @@ public class UnifiedGenotyperEngine { return new VariantCallContext(vc, false); } - public VariantCallContext calculateGenotypes(final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, final Map perReadAlleleLikelihoodMap) { + public VariantCallContext calculateGenotypes(final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, final Map perReadAlleleLikelihoodMap) { return calculateGenotypes(null, null, null, null, vc, model, perReadAlleleLikelihoodMap); } @@ -327,7 +327,7 @@ public class UnifiedGenotyperEngine { final Map stratifiedContexts, final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false,perReadAlleleLikelihoodMap); } @@ -346,7 +346,7 @@ public class UnifiedGenotyperEngine { final AlignmentContext rawContext, Map stratifiedContexts, final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, final boolean inheritAttributesFromInputVC, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index 3d287057c..79962a3e4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.indels; import com.google.java.contract.Ensures; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.clipping.ReadClipper; @@ -41,8 +41,8 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.variantcontext.Allele; +import java.io.PrintStream; import java.util.Arrays; -import java.util.HashMap; import java.util.LinkedHashMap; import java.util.Map; @@ -188,11 +188,14 @@ public class PairHMMIndelErrorModel { final LinkedHashMap haplotypeMap, final ReferenceContext ref, final int eventLength, - final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){ + final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap, + final double downsamplingFraction, + final PrintStream downsamplingLog) { final int numHaplotypes = haplotypeMap.size(); final int readCounts[] = new int[pileup.getNumberOfElements()]; final double[][] readLikelihoods = computeGeneralReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, perReadAlleleLikelihoodMap, readCounts); + perReadAlleleLikelihoodMap.performPerAlleleDownsampling(downsamplingFraction, downsamplingLog); return getDiploidHaplotypeLikelihoods(numHaplotypes, readCounts, readLikelihoods); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java new file mode 100644 index 000000000..e74684c53 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java @@ -0,0 +1,169 @@ +package org.broadinstitute.sting.gatk.walkers.qc; + +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.LocusWalker; +import org.broadinstitute.sting.gatk.walkers.TreeReducible; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; + +import java.io.PrintStream; +import java.util.List; + +/** + * Emits intervals in which the differences between the original and reduced bam quals are bigger epsilon (unless the quals of + * the reduced bam are above sufficient threshold) + * + *

Input

+ *

+ * The original and reduced BAM files. + *

+ * + *

Output

+ *

+ * A list of intervals in which the differences between the original and reduced bam quals are bigger epsilon. + *

+ * + *

Examples

+ * 
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -I:original original.bam \
+ *   -I:reduced reduced.bam \
+ *   -R ref.fasta \
+ *   -T AssessReducedQuals \
+ *   -o output.intervals
+ *
+ * + * @author ami + */ + +public class AssessReducedQuals extends LocusWalker implements TreeReducible { + + private static final String reduced = "reduced"; + private static final String original = "original"; + private static final int originalQualsIndex = 0; + private static final int reducedQualsIndex = 1; + + @Argument(fullName = "sufficientQualSum", shortName = "sufficientQualSum", doc = "When a reduced bam qual sum is above this threshold, it passes even without comparing to the non-reduced bam ", required = false) + public int sufficientQualSum = 600; + + @Argument(fullName = "qual_epsilon", shortName = "epsilon", doc = "when |Quals_reduced_bam - Quals_original_bam| > epsilon*Quals_original_bam we output this interval", required = false) + public int qual_epsilon = 0; + + @Argument(fullName = "debugLevel", shortName = "debug", doc = "debug mode on") + public int debugLevel = 0; + + @Output + protected PrintStream out; + + public void initialize() { + if (debugLevel != 0) + out.println(" Debug mode" + + "Debug:\tsufficientQualSum: "+sufficientQualSum+ "\n " + + "Debug:\tqual_epsilon: "+qual_epsilon); + } + + @Override + public boolean includeReadsWithDeletionAtLoci() { return true; } + + @Override + public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if ( tracker == null ) + return null; + + boolean reportLocus; + final int[] quals = getPileupQuals(context.getBasePileup()); + if (debugLevel != 0) + out.println("Debug:\tLocus Quals\t"+ref.getLocus()+"\toriginal\t"+quals[originalQualsIndex]+"\treduced\t"+quals[reducedQualsIndex]); + final int epsilon = MathUtils.fastRound(quals[originalQualsIndex]*qual_epsilon); + final int calcOriginalQuals = Math.min(quals[originalQualsIndex],sufficientQualSum); + final int calcReducedQuals = Math.min(quals[reducedQualsIndex],sufficientQualSum); + final int OriginalReducedQualDiff = calcOriginalQuals - calcReducedQuals; + reportLocus = OriginalReducedQualDiff > epsilon || OriginalReducedQualDiff < -1*epsilon; + if(debugLevel != 0 && reportLocus) + out.println("Debug:\tEmited Locus\t"+ref.getLocus()+"\toriginal\t"+quals[originalQualsIndex]+"\treduced\t"+quals[reducedQualsIndex]+"\tepsilon\t"+epsilon+"\tdiff\t"+OriginalReducedQualDiff); + + return reportLocus ? ref.getLocus() : null; + } + + private final int[] getPileupQuals(final ReadBackedPileup readPileup) { + + final int[] quals = new int[2]; + String[] printPileup = {"Debug 2:\toriginal pileup:\t"+readPileup.getLocation()+"\nDebug 2:----------------------------------\n", + "Debug 2:\t reduced pileup:\t"+readPileup.getLocation()+"\nDebug 2:----------------------------------\n"}; + + for( PileupElement p : readPileup ){ + final List tags = getToolkit().getReaderIDForRead(p.getRead()).getTags().getPositionalTags(); + if ( isGoodRead(p,tags) ){ + final int tempQual = (int)(p.getQual()) * p.getRepresentativeCount(); + final int tagIndex = getTagIndex(tags); + quals[tagIndex] += tempQual; + if(debugLevel == 2) + printPileup[tagIndex] += "\tDebug 2: ("+p+")\tMQ="+p.getMappingQual()+":QU="+p.getQual()+":RC="+p.getRepresentativeCount()+":OS="+p.getOffset()+"\n"; + } + } + if(debugLevel == 2){ + out.println(printPileup[originalQualsIndex]); + out.println(printPileup[reducedQualsIndex]); + } + return quals; + } + + private final boolean isGoodRead(PileupElement p, List tags){ + return !p.isDeletion() && (tags.contains(reduced) || (tags.contains(original) && (int)p.getQual() >= 20 && p.getMappingQual() >= 20)); + } + + private final int getTagIndex(List tags){ + return tags.contains(reduced) ? 1 : 0; + } + + @Override + public void onTraversalDone(GenomeLoc sum) { + if ( sum != null ) + out.println(sum); + } + + @Override + public GenomeLoc treeReduce(GenomeLoc lhs, GenomeLoc rhs) { + if ( lhs == null ) + return rhs; + + if ( rhs == null ) + return lhs; + + // if contiguous, just merge them + if ( lhs.contiguousP(rhs) ) + return getToolkit().getGenomeLocParser().createGenomeLoc(lhs.getContig(), lhs.getStart(), rhs.getStop()); + + // otherwise, print the lhs and start over with the rhs + out.println(lhs); + return rhs; + } + + @Override + public GenomeLoc reduceInit() { + return null; + } + + @Override + public GenomeLoc reduce(GenomeLoc value, GenomeLoc sum) { + if ( value == null ) + return sum; + + if ( sum == null ) + return value; + + // if contiguous, just merge them + if ( sum.contiguousP(value) ) + return getToolkit().getGenomeLocParser().createGenomeLoc(sum.getContig(), sum.getStart(), value.getStop()); + + // otherwise, print the sum and start over with the value + out.println(sum); + return value; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java index 5beeeb3e6..79b6e17f6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java @@ -245,24 +245,21 @@ public class GenotypeAndValidate extends RodWalker samples; + private enum GVstatus { + T, F, NONE + } + public static class CountedData { private long nAltCalledAlt = 0L; private long nAltCalledRef = 0L; @@ -336,8 +333,9 @@ public class GenotypeAndValidate extends RodWalker 0 && context.getBasePileup().getBases().length < minDepth)) { counter.nUncovered = 1L; - if (vcComp.getAttribute("GV").equals("T")) + final GVstatus status = getGVstatus(vcComp); + if ( status == GVstatus.T ) counter.nAltNotCalled = 1L; - else if (vcComp.getAttribute("GV").equals("F")) + else if ( status == GVstatus.F ) counter.nRefNotCalled = 1L; else counter.nNoStatusNotCalled = 1L; @@ -427,10 +426,11 @@ public class GenotypeAndValidate extends RodWalker extends NestedIntegerArray { } @Override - public void put( final T value, final int... keys ) { - super.put(value, keys); - + public boolean put( final T value, final int... keys ) { StringBuilder logEntry = new StringBuilder(); logEntry.append(logEntryLabel); @@ -116,5 +114,7 @@ public class LoggingNestedIntegerArray extends NestedIntegerArray { // PrintStream methods all use synchronized blocks internally, so our logging is thread-safe log.println(logEntry.toString()); + + return super.put(value, keys); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/collections/NestedIntegerArray.java b/public/java/src/org/broadinstitute/sting/utils/collections/NestedIntegerArray.java index 31d316555..050ed52ac 100755 --- a/public/java/src/org/broadinstitute/sting/utils/collections/NestedIntegerArray.java +++ b/public/java/src/org/broadinstitute/sting/utils/collections/NestedIntegerArray.java @@ -25,9 +25,11 @@ package org.broadinstitute.sting.utils.collections; +import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; +import java.util.Arrays; import java.util.List; /** @@ -38,18 +40,51 @@ import java.util.List; public class NestedIntegerArray { + private static Logger logger = Logger.getLogger(NestedIntegerArray.class); + protected final Object[] data; protected final int numDimensions; protected final int[] dimensions; + // Preallocate the first two dimensions to limit contention during tree traversals in put() + private static final int NUM_DIMENSIONS_TO_PREALLOCATE = 2; + public NestedIntegerArray(final int... dimensions) { numDimensions = dimensions.length; if ( numDimensions == 0 ) throw new ReviewedStingException("There must be at least one dimension to an NestedIntegerArray"); this.dimensions = dimensions.clone(); + int dimensionsToPreallocate = Math.min(dimensions.length, NUM_DIMENSIONS_TO_PREALLOCATE); + + logger.info(String.format("Creating NestedIntegerArray with dimensions %s", Arrays.toString(dimensions))); + logger.info(String.format("Pre-allocating first %d dimensions", dimensionsToPreallocate)); + data = new Object[dimensions[0]]; + preallocateArray(data, 0, dimensionsToPreallocate); + + logger.info(String.format("Done pre-allocating first %d dimensions", dimensionsToPreallocate)); + } + + /** + * Recursively allocate the first dimensionsToPreallocate dimensions of the tree + * + * Pre-allocating the first few dimensions helps limit contention during tree traversals in put() + * + * @param subarray current node in the tree + * @param dimension current level in the tree + * @param dimensionsToPreallocate preallocate only this many dimensions (starting from the first) + */ + private void preallocateArray( Object[] subarray, int dimension, int dimensionsToPreallocate ) { + if ( dimension >= dimensionsToPreallocate - 1 ) { + return; + } + + for ( int i = 0; i < subarray.length; i++ ) { + subarray[i] = new Object[dimensions[dimension + 1]]; + preallocateArray((Object[])subarray[i], dimension + 1, dimensionsToPreallocate); + } } public T get(final int... keys) { @@ -59,14 +94,30 @@ public class NestedIntegerArray { for( int i = 0; i < numNestedDimensions; i++ ) { if ( keys[i] >= dimensions[i] ) return null; + myData = (Object[])myData[keys[i]]; if ( myData == null ) return null; } + return (T)myData[keys[numNestedDimensions]]; } - public synchronized void put(final T value, final int... keys) { // WARNING! value comes before the keys! + /** + * Insert a value at the position specified by the given keys. + * + * This method is thread-safe, however the caller MUST check the + * return value to see if the put succeeded. This method RETURNS FALSE if + * the value could not be inserted because there already was a value present + * at the specified location. In this case the caller should do a get() to get + * the already-existing value and (potentially) update it. + * + * @param value value to insert + * @param keys keys specifying the location of the value in the tree + * @return true if the value was inserted, false if it could not be inserted because there was already + * a value at the specified position + */ + public boolean put(final T value, final int... keys) { // WARNING! value comes before the keys! if ( keys.length != numDimensions ) throw new ReviewedStingException("Exactly " + numDimensions + " keys should be passed to this NestedIntegerArray but " + keys.length + " were provided"); @@ -75,15 +126,35 @@ public class NestedIntegerArray { for ( int i = 0; i < numNestedDimensions; i++ ) { if ( keys[i] >= dimensions[i] ) throw new ReviewedStingException("Key " + keys[i] + " is too large for dimension " + i + " (max is " + (dimensions[i]-1) + ")"); - Object[] temp = (Object[])myData[keys[i]]; - if ( temp == null ) { - temp = new Object[dimensions[i+1]]; - myData[keys[i]] = temp; + + // If we're at or beyond the last dimension that was pre-allocated, we need to do a synchronized + // check to see if the next branch exists, and if it doesn't, create it + if ( i >= NUM_DIMENSIONS_TO_PREALLOCATE - 1 ) { + synchronized ( myData ) { + if ( myData[keys[i]] == null ) { + myData[keys[i]] = new Object[dimensions[i + 1]]; + } + } } - myData = temp; + + myData = (Object[])myData[keys[i]]; } - myData[keys[numNestedDimensions]] = value; + synchronized ( myData ) { // lock the bottom row while we examine and (potentially) update it + + // Insert the new value only if there still isn't any existing value in this position + if ( myData[keys[numNestedDimensions]] == null ) { + myData[keys[numNestedDimensions]] = value; + } + else { + // Already have a value for this leaf (perhaps another thread came along and inserted one + // while we traversed the tree), so return false to notify the caller that we didn't put + // the item + return false; + } + } + + return true; } public List getAllValues() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java similarity index 72% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java rename to public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java index a83adc275..22d249240 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java +++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java @@ -22,26 +22,29 @@ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.genotyper; +package org.broadinstitute.sting.utils.genotyper; -//import org.broadinstitute.sting.gatk.walkers.Requires; -import com.google.java.contract.Requires; +import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.variantcontext.Allele; +import java.io.PrintStream; +import java.lang.reflect.Constructor; import java.util.*; -public class PerReadAlleleLikelihoodMap { +public abstract class PerReadAlleleLikelihoodMap { + public static final double INDEL_LIKELIHOOD_THRESH = 0.1; - private List alleles; - private Map> likelihoodReadMap; - public PerReadAlleleLikelihoodMap() { - likelihoodReadMap = new LinkedHashMap>(); - alleles = new ArrayList(); - } + protected List alleles; + protected Map> likelihoodReadMap; + + public abstract void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log); + public abstract ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log); public void add(GATKSAMRecord read, Allele a, Double likelihood) { Map likelihoodMap; @@ -95,16 +98,6 @@ public class PerReadAlleleLikelihoodMap { public int getNumberOfStoredElements() { return likelihoodReadMap.size(); } - /** - * Returns list of reads greedily associated with a particular allele. - * Needs to loop for each read, and assign to each allele - * @param a Desired allele - * @return - */ - @Requires("a!=null") - public List getReadsAssociatedWithAllele(Allele a) { - return null; - } public Map getLikelihoodsAssociatedWithPileupElement(PileupElement p) { if (!likelihoodReadMap.containsKey(p.getRead())) @@ -129,4 +122,16 @@ public class PerReadAlleleLikelihoodMap { } return (maxLike - prevMaxLike > INDEL_LIKELIHOOD_THRESH ? mostLikelyAllele : Allele.NO_CALL ); } - } + + public static PerReadAlleleLikelihoodMap getBestAvailablePerReadAlleleLikelihoodMap() { + final Class PerReadAlleleLikelihoodMapClass = GATKLiteUtils.getProtectedClassIfAvailable(PerReadAlleleLikelihoodMap.class); + try { + Constructor constructor = PerReadAlleleLikelihoodMapClass.getDeclaredConstructor((Class[])null); + constructor.setAccessible(true); + return (PerReadAlleleLikelihoodMap)constructor.newInstance(); + } + catch (Exception e) { + throw new ReviewedStingException("Unable to create RecalibrationEngine class instance " + PerReadAlleleLikelihoodMapClass.getSimpleName()); + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java new file mode 100644 index 000000000..7db818592 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java @@ -0,0 +1,46 @@ +/* + * Copyright (c) 2011 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ +package org.broadinstitute.sting.utils.genotyper; + + +import org.broadinstitute.sting.utils.classloader.PublicPackageSource; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.variantcontext.Allele; + +import java.io.PrintStream; +import java.util.*; + +public class StandardPerReadAlleleLikelihoodMap extends PerReadAlleleLikelihoodMap implements PublicPackageSource { + + public StandardPerReadAlleleLikelihoodMap() { + likelihoodReadMap = new LinkedHashMap>(); + alleles = new ArrayList(); + } + + // not implemented in the standard version + public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) {} + public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { return pileup; } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java index 7ad9302a8..2f9387acb 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java @@ -116,9 +116,12 @@ public class BaseRecalibration { // Compute all covariates for the read // TODO -- the need to clear here suggests there's an error in the indexing / assumption code // TODO -- for BI and DI. Perhaps due to the indel buffer size on the ends of the reads? - // TODO -- the output varies with -nt 1 and -nt 2 if you don't call clear here - // TODO -- needs to be fixed. - final ReadCovariates readCovariates = readCovariatesCache.get().clear(); + // TODO -- the output varies depending on whether we clear or not + //final ReadCovariates readCovariates = readCovariatesCache.get().clear(); + + // the original code -- doesn't do any clearing + final ReadCovariates readCovariates = readCovariatesCache.get(); + RecalUtils.computeCovariates(read, requestedCovariates, readCovariates); for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java index 85568dac9..29c15adf7 100755 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java @@ -66,7 +66,9 @@ public class ReadGroupCovariate implements RequiredCovariate { } @Override - public String formatKey(final int key) { + public synchronized String formatKey(final int key) { + // This method is synchronized so that we don't attempt to do a get() + // from the reverse lookup table while that table is being updated return readGroupReverseLookupTable.get(key); } @@ -76,17 +78,32 @@ public class ReadGroupCovariate implements RequiredCovariate { } private int keyForReadGroup(final String readGroupId) { - if (!readGroupLookupTable.containsKey(readGroupId)) { - readGroupLookupTable.put(readGroupId, nextId); - readGroupReverseLookupTable.put(nextId, readGroupId); - nextId++; + // Rather than synchronize this entire method (which would be VERY expensive for walkers like the BQSR), + // synchronize only the table updates. + + // Before entering the synchronized block, check to see if this read group is not in our tables. + // If it's not, either we will have to insert it, OR another thread will insert it first. + // This preliminary check avoids doing any synchronization most of the time. + if ( ! readGroupLookupTable.containsKey(readGroupId) ) { + + synchronized ( this ) { + + // Now we need to make sure the key is STILL not there, since another thread may have come along + // and inserted it while we were waiting to enter this synchronized block! + if ( ! readGroupLookupTable.containsKey(readGroupId) ) { + readGroupLookupTable.put(readGroupId, nextId); + readGroupReverseLookupTable.put(nextId, readGroupId); + nextId++; + } + } } return readGroupLookupTable.get(readGroupId); } @Override - public int maximumKeyValue() { + public synchronized int maximumKeyValue() { + // Synchronized so that we don't query table size while the tables are being updated return readGroupLookupTable.size() - 1; } diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/ThreadLocalArray.java b/public/java/src/org/broadinstitute/sting/utils/threading/ThreadLocalArray.java new file mode 100644 index 000000000..cc50152ac --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/threading/ThreadLocalArray.java @@ -0,0 +1,64 @@ +/* + * Copyright (c) 2012, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.threading; + +import java.lang.reflect.Array; + +/** + * ThreadLocal implementation for arrays + * + * Example usage: + * + * private ThreadLocal threadLocalByteArray = new ThreadLocalArray(length, byte.class); + * .... + * byte[] byteArray = threadLocalByteArray.get(); + * + * @param the type of the array itself (eg., int[], double[], etc.) + * + * @author David Roazen + */ +public class ThreadLocalArray extends ThreadLocal { + private int arraySize; + private Class arrayElementType; + + /** + * Create a new ThreadLocalArray + * + * @param arraySize desired length of the array + * @param arrayElementType type of the elements within the array (eg., Byte.class, Integer.class, etc.) + */ + public ThreadLocalArray( int arraySize, Class arrayElementType ) { + super(); + + this.arraySize = arraySize; + this.arrayElementType = arrayElementType; + } + + @Override + @SuppressWarnings("unchecked") + protected T initialValue() { + return (T)Array.newInstance(arrayElementType, arraySize); + } +} diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index dee54b9f8..8eb1c4657 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -480,4 +480,20 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { Arrays.asList(md5)); executeTest("test calling on a ReducedRead BAM with " + model, spec); } + + // -------------------------------------------------------------------------------------------------------------- + // + // testing contamination down-sampling + // + // -------------------------------------------------------------------------------------------------------------- + + @Test + public void testContaminationDownsampling() { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --contamination_percentage_to_filter 0.20", 1, + Arrays.asList("27dd04159e06d9524fb8a4eef41f96ae")); + executeTest("test contamination_percentage_to_filter 0.20", spec); + } + + } diff --git a/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerUnitTest.java index 2ba2da734..af2e18ad9 100644 --- a/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerUnitTest.java @@ -23,6 +23,7 @@ import java.util.List; * To change this template use File | Settings | File Templates. */ public class NanoSchedulerUnitTest extends BaseTest { + private final static boolean DEBUG = false; private final static boolean debug = false; public static final int NANO_SCHEDULE_MAX_RUNTIME = 30000; @@ -30,19 +31,22 @@ public class NanoSchedulerUnitTest extends BaseTest { @Override public Integer apply(Integer input) { return input * 2; } } + private static void maybeDelayMe(final int input) { + try { + if ( input % 7 == 0 ) { + final int milliToSleep = (input % 10); + //System.out.printf("Sleeping %d millseconds%n", milliToSleep); + Thread.sleep(milliToSleep); + } + } catch ( InterruptedException ex ) { + throw new RuntimeException(ex); + } + } + private static class Map2xWithDelays extends Map2x { @Override public Integer apply(Integer input) { - try { - if ( input % 7 == 0 ) { - final int milliToSleep = (input % 10); - //System.out.printf("Sleeping %d millseconds%n", milliToSleep); - Thread.sleep(milliToSleep); - } - - return input * 2; - } catch ( InterruptedException ex ) { - throw new RuntimeException(ex); - } + maybeDelayMe(input); + return input * 2; } } @@ -117,10 +121,12 @@ public class NanoSchedulerUnitTest extends BaseTest { } static NanoSchedulerBasicTest exampleTest = null; + static NanoSchedulerBasicTest exampleTestWithDelays = null; @BeforeSuite public void setUp() throws Exception { exampleTest = new NanoSchedulerBasicTest(10, 2, 1, 10, false); + exampleTestWithDelays = new NanoSchedulerBasicTest(10, 2, 1, 10, true); } @DataProvider(name = "NanoSchedulerBasicTest") @@ -151,14 +157,14 @@ public class NanoSchedulerUnitTest extends BaseTest { return NanoSchedulerBasicTest.getTests(NanoSchedulerBasicTest.class); } - @Test(enabled = true, dataProvider = "NanoSchedulerBasicTest", timeOut = NANO_SCHEDULE_MAX_RUNTIME) + @Test(enabled = true && ! DEBUG, dataProvider = "NanoSchedulerBasicTest", timeOut = NANO_SCHEDULE_MAX_RUNTIME) public void testSingleThreadedNanoScheduler(final NanoSchedulerBasicTest test) throws InterruptedException { logger.warn("Running " + test); if ( test.nThreads == 1 ) testNanoScheduler(test); } - @Test(enabled = true, dataProvider = "NanoSchedulerBasicTest", timeOut = NANO_SCHEDULE_MAX_RUNTIME, dependsOnMethods = "testSingleThreadedNanoScheduler") + @Test(enabled = true && ! DEBUG, dataProvider = "NanoSchedulerBasicTest", timeOut = NANO_SCHEDULE_MAX_RUNTIME, dependsOnMethods = "testSingleThreadedNanoScheduler") public void testMultiThreadedNanoScheduler(final NanoSchedulerBasicTest test) throws InterruptedException { logger.warn("Running " + test); if ( test.nThreads >= 1 ) @@ -195,7 +201,7 @@ public class NanoSchedulerUnitTest extends BaseTest { } } - @Test(enabled = true, dataProvider = "NanoSchedulerBasicTest", dependsOnMethods = "testMultiThreadedNanoScheduler", timeOut = NANO_SCHEDULE_MAX_RUNTIME) + @Test(enabled = true && ! DEBUG, dataProvider = "NanoSchedulerBasicTest", dependsOnMethods = "testMultiThreadedNanoScheduler", timeOut = NANO_SCHEDULE_MAX_RUNTIME) public void testNanoSchedulerInLoop(final NanoSchedulerBasicTest test) throws InterruptedException { if ( test.bufferSize > 1) { logger.warn("Running " + test); @@ -213,7 +219,7 @@ public class NanoSchedulerUnitTest extends BaseTest { } } - @Test(timeOut = NANO_SCHEDULE_MAX_RUNTIME) + @Test(enabled = true && ! DEBUG, timeOut = NANO_SCHEDULE_MAX_RUNTIME) public void testShutdown() throws InterruptedException { final NanoScheduler nanoScheduler = new NanoScheduler(1, 2); Assert.assertFalse(nanoScheduler.isShutdown(), "scheduler should be alive"); @@ -221,38 +227,78 @@ public class NanoSchedulerUnitTest extends BaseTest { Assert.assertTrue(nanoScheduler.isShutdown(), "scheduler should be dead"); } - @Test(expectedExceptions = IllegalStateException.class, timeOut = NANO_SCHEDULE_MAX_RUNTIME) + @Test(enabled = true && ! DEBUG, expectedExceptions = IllegalStateException.class, timeOut = NANO_SCHEDULE_MAX_RUNTIME) public void testShutdownExecuteFailure() throws InterruptedException { final NanoScheduler nanoScheduler = new NanoScheduler(1, 2); nanoScheduler.shutdown(); nanoScheduler.execute(exampleTest.makeReader(), exampleTest.makeMap(), exampleTest.initReduce(), exampleTest.makeReduce()); } - @Test(expectedExceptions = NullPointerException.class, timeOut = 10000, invocationCount = 50) + @DataProvider(name = "NanoSchedulerInputExceptionTest") + public Object[][] createNanoSchedulerInputExceptionTest() { + List tests = new ArrayList(); + + + for ( final int bufSize : Arrays.asList(100) ) { + for ( final int nThreads : Arrays.asList(8) ) { + for ( final boolean addDelays : Arrays.asList(true, false) ) { + final NanoSchedulerBasicTest test = new NanoSchedulerBasicTest(bufSize, nThreads, 1, 1000000, false); + final int maxN = addDelays ? 10000 : 100000; + for ( int nElementsBeforeError = 0; nElementsBeforeError < maxN; nElementsBeforeError += Math.max(nElementsBeforeError / 10, 1) ) { + tests.add(new Object[]{nElementsBeforeError, test, addDelays}); + } + } + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test(enabled = true, expectedExceptions = NullPointerException.class, timeOut = 10000) public void testInputErrorIsThrown_NPE() throws InterruptedException { - executeTestErrorThrowingInput(new NullPointerException()); + executeTestErrorThrowingInput(10, new NullPointerException(), exampleTest, false); } - @Test(expectedExceptions = ReviewedStingException.class, timeOut = 10000, invocationCount = 50) + @Test(enabled = true, expectedExceptions = ReviewedStingException.class, timeOut = 10000) public void testInputErrorIsThrown_RSE() throws InterruptedException { - executeTestErrorThrowingInput(new ReviewedStingException("test")); + executeTestErrorThrowingInput(10, new ReviewedStingException("test"), exampleTest, false); } - private void executeTestErrorThrowingInput(final RuntimeException ex) { - final NanoScheduler nanoScheduler = new NanoScheduler(1, 2); - nanoScheduler.execute(new ErrorThrowingIterator(ex), exampleTest.makeMap(), exampleTest.initReduce(), exampleTest.makeReduce()); + @Test(enabled = true, expectedExceptions = NullPointerException.class, dataProvider = "NanoSchedulerInputExceptionTest", timeOut = 10000, invocationCount = 1) + public void testInputErrorDoesntDeadlock(final int nElementsBeforeError, final NanoSchedulerBasicTest test, final boolean addDelays ) throws InterruptedException { + executeTestErrorThrowingInput(nElementsBeforeError, new NullPointerException(), test, addDelays); + } + + private void executeTestErrorThrowingInput(final int nElementsBeforeError, final RuntimeException ex, final NanoSchedulerBasicTest test, final boolean addDelays) { + logger.warn("executeTestErrorThrowingInput " + nElementsBeforeError + " ex=" + ex + " test=" + test + " addInputDelays=" + addDelays); + final NanoScheduler nanoScheduler = test.makeScheduler(); + nanoScheduler.execute(new ErrorThrowingIterator(nElementsBeforeError, ex, addDelays), test.makeMap(), test.initReduce(), test.makeReduce()); } private static class ErrorThrowingIterator implements Iterator { + final int nElementsBeforeError; + final boolean addDelays; + int i = 0; final RuntimeException ex; - private ErrorThrowingIterator(RuntimeException ex) { + private ErrorThrowingIterator(final int nElementsBeforeError, RuntimeException ex, boolean addDelays) { + this.nElementsBeforeError = nElementsBeforeError; this.ex = ex; + this.addDelays = addDelays; } - @Override public boolean hasNext() { throw ex; } - @Override public Integer next() { throw ex; } - @Override public void remove() { throw ex; } + @Override public boolean hasNext() { return true; } + @Override public Integer next() { + if ( i++ > nElementsBeforeError ) { + throw ex; + } else if ( addDelays ) { + maybeDelayMe(i); + return i; + } else { + return i; + } + } + @Override public void remove() { throw new UnsupportedOperationException("x"); } } public static void main(String [ ] args) { diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala index 5e66520ca..9e8815762 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala @@ -136,7 +136,14 @@ class GATKResourcesBundle extends QScript { addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/GoldStandardIndel/gold.standard.indel.MillsAnd1000G.b37.vcf", "Mills_and_1000G_gold_standard.indels", b37, true, false)) - + + // + // CEU trio (NA12878,NA12891,NA12892) best practices results (including PBT) + // + + addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/callsets/CEUtrio_BestPractices/current/CEUTrio.HiSeq.WGS.b37.UG.snps_and_indels.recalibrated.filtered.phaseByTransmission.vcf", + "CEUTrio.HiSeq.WGS.b37.UG.bestPractices.phaseByTransmission",b37,true,false)) + // // example call set for wiki tutorial //