Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
This commit is contained in:
Chris Hartl
commit
37eb6c92bf
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@ -253,7 +253,6 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
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intervalList.addAll(toolkit.getIntervals());
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// todo -- rework the whole NO_PG_TAG thing
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final boolean preSorted = true;
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final boolean indexOnTheFly = true;
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final boolean keep_records = true;
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@ -220,7 +220,6 @@ public class SlidingWindow {
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regions = findVariantRegions(0, breakpoint, markedSites.getVariantSiteBitSet(), !forceClose);
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}
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// todo -- can be more aggressive here removing until the NEW window header start location after closing the variant regions
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while (!readsInWindow.isEmpty() && readsInWindow.first().getSoftEnd() < windowHeaderStartLocation) {
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readsInWindow.pollFirst();
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}
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@ -607,9 +606,7 @@ public class SlidingWindow {
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toRemove.add(read);
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}
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}
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for (GATKSAMRecord read : toRemove) {
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readsInWindow.remove(read);
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}
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removeReadsFromWindow(toRemove);
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}
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return allReads;
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}
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@ -805,9 +802,8 @@ public class SlidingWindow {
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hetReads.add(finalizeRunningConsensus());
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}
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for (GATKSAMRecord read : toRemove) {
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readsInWindow.remove(read);
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}
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removeReadsFromWindow(toRemove);
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return hetReads;
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}
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@ -924,5 +920,11 @@ public class SlidingWindow {
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}
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}
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}
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private void removeReadsFromWindow (List<GATKSAMRecord> readsToRemove) {
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for (GATKSAMRecord read : readsToRemove) {
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readsInWindow.remove(read);
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}
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}
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}
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@ -41,13 +41,11 @@ import java.util.*;
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public class GenotypingEngine {
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private final boolean DEBUG;
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private final boolean OUTPUT_FULL_HAPLOTYPE_SEQUENCE;
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private final static List<Allele> noCall = new ArrayList<Allele>(); // used to noCall all genotypes until the exact model is applied
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private final static Allele SYMBOLIC_UNASSEMBLED_EVENT_ALLELE = Allele.create("<UNASSEMBLED_EVENT>", false);
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public GenotypingEngine( final boolean DEBUG, final boolean OUTPUT_FULL_HAPLOTYPE_SEQUENCE ) {
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public GenotypingEngine( final boolean DEBUG ) {
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this.DEBUG = DEBUG;
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this.OUTPUT_FULL_HAPLOTYPE_SEQUENCE = OUTPUT_FULL_HAPLOTYPE_SEQUENCE;
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noCall.add(Allele.NO_CALL);
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}
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@ -131,14 +131,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
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@Argument(fullName="minPruning", shortName="minPruning", doc = "The minimum allowed pruning factor in assembly graph. Paths with <= X supporting kmers are pruned from the graph", required = false)
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protected int MIN_PRUNE_FACTOR = 1;
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@Advanced
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@Argument(fullName="genotypeFullActiveRegion", shortName="genotypeFullActiveRegion", doc = "If specified, alternate alleles are considered to be the full active region for the purposes of genotyping", required = false)
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protected boolean GENOTYPE_FULL_ACTIVE_REGION = false;
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@Advanced
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@Argument(fullName="fullHaplotype", shortName="fullHaplotype", doc = "If specified, output the full haplotype sequence instead of converting to individual variants w.r.t. the reference", required = false)
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protected boolean OUTPUT_FULL_HAPLOTYPE_SEQUENCE = false;
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@Advanced
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@Argument(fullName="gcpHMM", shortName="gcpHMM", doc="Flat gap continuation penalty for use in the Pair HMM", required = false)
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protected int gcpHMM = 10;
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@ -248,10 +240,11 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
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// create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested
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UnifiedArgumentCollection simpleUAC = new UnifiedArgumentCollection(UAC);
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simpleUAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY; // low values used for isActive determination only, default/user-specified values used for actual calling
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simpleUAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY; // low values used for isActive determination only, default/user-specified values used for actual calling
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simpleUAC.STANDARD_CONFIDENCE_FOR_CALLING = Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_CALLING );
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simpleUAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING );
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simpleUAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY;
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simpleUAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY;
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simpleUAC.STANDARD_CONFIDENCE_FOR_CALLING = Math.min( 4.0, UAC.STANDARD_CONFIDENCE_FOR_CALLING ); // low values used for isActive determination only, default/user-specified values used for actual calling
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simpleUAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.min( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING ); // low values used for isActive determination only, default/user-specified values used for actual calling
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simpleUAC.CONTAMINATION_FRACTION = 0.0;
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simpleUAC.exactCallsLog = null;
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UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
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@ -273,15 +266,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
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VCFConstants.GENOTYPE_QUALITY_KEY,
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VCFConstants.DEPTH_KEY,
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VCFConstants.GENOTYPE_PL_KEY);
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// header lines for the experimental HaplotypeCaller-specific annotations
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headerInfo.add(new VCFInfoHeaderLine("NVH", 1, VCFHeaderLineType.Integer, "Number of variants found on the haplotype that contained this variant"));
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headerInfo.add(new VCFInfoHeaderLine("NumHapEval", 1, VCFHeaderLineType.Integer, "Number of haplotypes that were chosen for evaluation in this active region"));
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headerInfo.add(new VCFInfoHeaderLine("NumHapAssembly", 1, VCFHeaderLineType.Integer, "Number of haplotypes created during the assembly of this active region"));
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headerInfo.add(new VCFInfoHeaderLine("ActiveRegionSize", 1, VCFHeaderLineType.Integer, "Number of base pairs that comprise this active region"));
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headerInfo.add(new VCFInfoHeaderLine("EVENTLENGTH", 1, VCFHeaderLineType.Integer, "Max length of all the alternate alleles"));
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headerInfo.add(new VCFInfoHeaderLine("TYPE", 1, VCFHeaderLineType.String, "Type of event: SNP or INDEL"));
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headerInfo.add(new VCFInfoHeaderLine("extType", 1, VCFHeaderLineType.String, "Extended type of event: SNP, MNP, INDEL, or COMPLEX"));
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headerInfo.add(new VCFInfoHeaderLine("QDE", 1, VCFHeaderLineType.Float, "QD value divided by the number of variants found on the haplotype that contained this variant"));
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// FILTER fields are added unconditionally as it's not always 100% certain the circumstances
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// where the filters are used. For example, in emitting all sites the lowQual field is used
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@ -298,7 +282,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
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assemblyEngine = new SimpleDeBruijnAssembler( DEBUG, graphWriter );
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likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM );
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genotypingEngine = new GenotypingEngine( DEBUG, OUTPUT_FULL_HAPLOTYPE_SEQUENCE );
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genotypingEngine = new GenotypingEngine( DEBUG );
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}
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//---------------------------------------------------------------------------------------------------------------
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@ -428,43 +412,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
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final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = LikelihoodCalculationEngine.partitionReadsBasedOnLikelihoods( getToolkit().getGenomeLocParser(), perSampleReadList, perSampleFilteredReadList, callResult, UG_engine.getUAC().CONTAMINATION_FRACTION, UG_engine.getUAC().contaminationLog );
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final VariantContext annotatedCall = annotationEngine.annotateContext(stratifiedReadMap, callResult.getFirst());
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final Map<String, Object> myAttributes = new LinkedHashMap<String, Object>(annotatedCall.getAttributes());
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if( !GENOTYPE_FULL_ACTIVE_REGION ) {
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// add some custom annotations to the calls
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// Calculate the number of variants on the haplotype
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int maxNumVar = 0;
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for( final Allele allele : callResult.getFirst().getAlleles() ) {
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if( !allele.isReference() ) {
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for( final Haplotype haplotype : callResult.getSecond().get(allele) ) {
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final int numVar = haplotype.getEventMap().size();
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if( numVar > maxNumVar ) { maxNumVar = numVar; }
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}
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}
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}
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// Calculate the event length
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int maxLength = 0;
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for ( final Allele a : annotatedCall.getAlternateAlleles() ) {
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final int length = a.length() - annotatedCall.getReference().length();
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if( Math.abs(length) > Math.abs(maxLength) ) { maxLength = length; }
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}
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myAttributes.put("NVH", maxNumVar);
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myAttributes.put("NumHapEval", bestHaplotypes.size());
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myAttributes.put("NumHapAssembly", haplotypes.size());
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myAttributes.put("ActiveRegionSize", activeRegion.getLocation().size());
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myAttributes.put("EVENTLENGTH", maxLength);
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myAttributes.put("TYPE", (annotatedCall.isSNP() || annotatedCall.isMNP() ? "SNP" : "INDEL") );
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myAttributes.put("extType", annotatedCall.getType().toString() );
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//if( likelihoodCalculationEngine.haplotypeScore != null ) {
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// myAttributes.put("HaplotypeScore", String.format("%.4f", likelihoodCalculationEngine.haplotypeScore));
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//}
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if( annotatedCall.hasAttribute("QD") ) {
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myAttributes.put("QDE", String.format("%.2f", Double.parseDouble((String)annotatedCall.getAttribute("QD")) / ((double)maxNumVar)) );
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}
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}
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vcfWriter.add( new VariantContextBuilder(annotatedCall).attributes(myAttributes).make() );
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}
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@ -520,6 +467,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
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if( postAdapterRead != null && !postAdapterRead.isEmpty() && postAdapterRead.getCigar().getReadLength() > 0 ) {
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final GATKSAMRecord clippedRead = ReadClipper.hardClipLowQualEnds( postAdapterRead, MIN_TAIL_QUALITY );
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// protect against INTERVALS with abnormally high coverage
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// BUGBUG: remove when positinal downsampler is hooked up to ART/HC
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if( clippedRead.getReadLength() > 0 && activeRegion.size() < samplesList.size() * DOWNSAMPLE_PER_SAMPLE_PER_REGION ) {
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activeRegion.add(clippedRead);
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}
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@ -169,7 +169,6 @@ public class LikelihoodCalculationEngine {
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}
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// compute the diploid haplotype likelihoods
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// todo - needs to be generalized to arbitrary ploidy, cleaned and merged with PairHMMIndelErrorModel code
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for( int iii = 0; iii < numHaplotypes; iii++ ) {
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for( int jjj = 0; jjj <= iii; jjj++ ) {
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for( final Haplotype iii_mapped : haplotypeMapping.get(alleleOrdering.get(iii)) ) {
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@ -21,18 +21,19 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotypeCallerMultiSample() {
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HCTest(CEUTRIO_BAM, "", "56aa4b84606b6b0b7dc78a383974d1b3");
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HCTest(CEUTRIO_BAM, "", "2b39732ff8e0de5bc2ae949aaf7a6f21");
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}
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@Test
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public void testHaplotypeCallerSingleSample() {
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HCTest(NA12878_BAM, "", "baabae06c85d416920be434939124d7f");
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HCTest(NA12878_BAM, "", "8b217638ff585effb9cc70e9a9aa544f");
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}
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// TODO -- add more tests for GGA mode, especially with input alleles that are complex variants and/or not trimmed
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@Test
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public void testHaplotypeCallerMultiSampleGGA() {
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HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "f2d0309fdf50d5827e9c60ed0dd07e3f");
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HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
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||||
"541aa8291f03ba33bd1ad3d731fd5657");
|
||||
}
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private void HCTestComplexVariants(String bam, String args, String md5) {
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@ -43,7 +44,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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|
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@Test
|
||||
public void testHaplotypeCallerMultiSampleComplex() {
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HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "966d338f423c86a390d685aa6336ec69");
|
||||
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "fd7170cbde7df04d4fbe1da7903c31c6");
|
||||
}
|
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|
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private void HCTestSymbolicVariants(String bam, String args, String md5) {
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|
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@ -54,7 +55,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
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|
||||
@Test
|
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public void testHaplotypeCallerSingleSampleSymbolic() {
|
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HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "7fbc6b9e27e374f2ffe4be952d88c7c6");
|
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HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "99456fc7207c1fe9f367a0d0afae87cd");
|
||||
}
|
||||
|
||||
private void HCTestIndelQualityScores(String bam, String args, String md5) {
|
||||
|
|
@ -65,20 +66,20 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
|
||||
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "2581e760279291a3901a506d060bfac8");
|
||||
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "6c1631785b3f832aecab1a99f0454762");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void HCTestProblematicReadsModifiedInActiveRegions() {
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("788176e1717bd28fc7cbc8e3efbb6100"));
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ec437d2d9f3ae07d155983be0155c8ed"));
|
||||
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void HCTestStructuralIndels() {
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("96ab8253d242b851ccfc218759f79784"));
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("237601bbc39694c7413a332cbb656c8e"));
|
||||
executeTest("HCTestStructuralIndels: ", spec);
|
||||
}
|
||||
|
||||
|
|
@ -92,7 +93,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void HCTestReducedBam() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
|
||||
Arrays.asList("425f1a0fb00d7145edf1c55e54346fae"));
|
||||
Arrays.asList("40bf739fb2b1743642498efe79ea6342"));
|
||||
executeTest("HC calling on a ReducedRead BAM", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
|
|||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
import org.broadinstitute.sting.utils.help.ApplicationDetails;
|
||||
import org.broadinstitute.sting.utils.help.HelpFormatter;
|
||||
import org.broadinstitute.sting.utils.help.HelpUtils;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.*;
|
||||
|
|
@ -288,7 +289,7 @@ public abstract class CommandLineProgram {
|
|||
*/
|
||||
private static void printDocumentationReference() {
|
||||
errorPrintf("Visit our website and forum for extensive documentation and answers to %n");
|
||||
errorPrintf("commonly asked questions http://www.broadinstitute.org/gatk%n");
|
||||
errorPrintf("commonly asked questions " + HelpUtils.BASE_GATK_URL + "%n");
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
|
|||
import org.broadinstitute.sting.utils.help.ApplicationDetails;
|
||||
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
|
||||
import org.broadinstitute.sting.utils.help.GATKDocUtils;
|
||||
import org.broadinstitute.sting.utils.help.HelpUtils;
|
||||
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
|
||||
|
||||
import java.util.*;
|
||||
|
|
@ -160,7 +161,7 @@ public class CommandLineGATK extends CommandLineExecutable {
|
|||
List<String> header = new ArrayList<String>();
|
||||
header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime()));
|
||||
header.add("Copyright (c) 2010 The Broad Institute");
|
||||
header.add("For support and documentation go to http://www.broadinstitute.org/gatk");
|
||||
header.add("For support and documentation go to " + HelpUtils.BASE_GATK_URL);
|
||||
return header;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -25,11 +25,9 @@
|
|||
|
||||
package org.broadinstitute.sting.gatk.filters;
|
||||
|
||||
import com.google.common.base.Function;
|
||||
import com.google.common.collect.Collections2;
|
||||
import org.broadinstitute.sting.utils.Utils;
|
||||
import org.broadinstitute.sting.utils.classloader.PluginManager;
|
||||
import org.broadinstitute.sting.utils.help.GATKDocUtils;
|
||||
import org.broadinstitute.sting.utils.help.HelpUtils;
|
||||
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
|
|
@ -73,7 +71,7 @@ public class FilterManager extends PluginManager<ReadFilter> {
|
|||
|
||||
return String.format("Read filter %s not found. Available read filters:%n%n%s%n%n%s",pluginName,
|
||||
userFriendlyListofReadFilters(availableFilters),
|
||||
"Please consult the GATK Documentation (http://www.broadinstitute.org/gatk/gatkdocs/) for more information.");
|
||||
"Please consult the GATK Documentation (" + HelpUtils.GATK_DOCS_URL + ") for more information.");
|
||||
}
|
||||
|
||||
private String userFriendlyListofReadFilters(List<Class<? extends ReadFilter>> filters) {
|
||||
|
|
|
|||
|
|
@ -80,7 +80,6 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
|
|||
}
|
||||
|
||||
// skip this location -- it's not part of our engine intervals
|
||||
// TODO -- this is dangerously slow with current overlaps implementation : GSA-649 / GenomeLocSortedSet.overlaps is crazy slow
|
||||
if ( outsideEngineIntervals(location) )
|
||||
continue;
|
||||
|
||||
|
|
|
|||
|
|
@ -29,7 +29,7 @@ public class MappingQualityRankSumTest extends RankSumTest implements StandardAn
|
|||
final List<Double> refQuals, final List<Double> altQuals) {
|
||||
|
||||
if (pileup != null && likelihoodMap == null) {
|
||||
// no per-read likelihoods available:
|
||||
// old UG snp-only path through the annotations
|
||||
for ( final PileupElement p : pileup ) {
|
||||
if ( isUsableBase(p) ) {
|
||||
if ( allAlleles.get(0).equals(Allele.create(p.getBase(), true)) ) {
|
||||
|
|
@ -43,14 +43,13 @@ public class MappingQualityRankSumTest extends RankSumTest implements StandardAn
|
|||
}
|
||||
for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : likelihoodMap.getLikelihoodReadMap().entrySet()) {
|
||||
final Allele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
|
||||
// BUGBUG: There needs to be a comparable isUsableBase check here
|
||||
if (a.isNoCall())
|
||||
continue; // read is non-informative
|
||||
if (a.isReference())
|
||||
refQuals.add((double)el.getKey().getMappingQuality());
|
||||
else if (allAlleles.contains(a))
|
||||
altQuals.add((double)el.getKey().getMappingQuality());
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -49,7 +49,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR
|
|||
ReadBackedPileup pileup = null;
|
||||
|
||||
|
||||
if (stratifiedContexts != null) {
|
||||
if (stratifiedContexts != null) { // the old UG SNP-only path through the annotations
|
||||
final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
|
||||
if ( context != null )
|
||||
pileup = context.getBasePileup();
|
||||
|
|
|
|||
|
|
@ -39,7 +39,7 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio
|
|||
final List<Double> refQuals, final List<Double> altQuals) {
|
||||
|
||||
if (alleleLikelihoodMap == null) {
|
||||
// use fast SNP-based version if we don't have per-read allele likelihoods
|
||||
// use old UG SNP-based version if we don't have per-read allele likelihoods
|
||||
for ( final PileupElement p : pileup ) {
|
||||
if ( isUsableBase(p) ) {
|
||||
int readPos = AlignmentUtils.calcAlignmentByteArrayOffset(p.getRead().getCigar(), p, 0, 0);
|
||||
|
|
|
|||
|
|
@ -282,7 +282,8 @@ public class DiffEngine {
|
|||
// now that we have a specific list of values we want to show, display them
|
||||
GATKReport report = new GATKReport();
|
||||
final String tableName = "differences";
|
||||
report.addTable(tableName, "Summarized differences between the master and test files. See http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information", 3);
|
||||
// TODO for Geraldine -- link needs to be updated below
|
||||
report.addTable(tableName, "Summarized differences between the master and test files. See [ask Geraldine to fix link to DiffEngine wiki] for more information", 3);
|
||||
final GATKReportTable table = report.getTable(tableName);
|
||||
table.addColumn("Difference");
|
||||
table.addColumn("NumberOfOccurrences");
|
||||
|
|
|
|||
|
|
@ -138,7 +138,8 @@ public class DiffObjects extends RodWalker<Integer, Integer> {
|
|||
/**
|
||||
* Writes out a file of the DiffEngine format:
|
||||
*
|
||||
* http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
|
||||
* TODO for Geraldine -- link needs to be updated below (and also in SelectVariants and RefSeqCodec GATK docs)
|
||||
* http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
|
||||
*/
|
||||
@Output(doc="File to which results should be written",required=true)
|
||||
protected PrintStream out;
|
||||
|
|
|
|||
|
|
@ -47,6 +47,12 @@ import java.util.List;
|
|||
* <p>
|
||||
* Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s).
|
||||
* Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'.
|
||||
*
|
||||
* The output format can be partially controlled using the provided command-line arguments.
|
||||
* Specify intervals with the usual -L argument to output only the reference bases within your intervals.
|
||||
* Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a
|
||||
* separate fasta sequence (named numerically in order).
|
||||
*
|
||||
* Several important notes:
|
||||
* 1) if there are multiple variants that start at a site, it chooses one of them randomly.
|
||||
* 2) when there are overlapping indels (but with different start positions) only the first will be chosen.
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ import java.util.Set;
|
|||
/**
|
||||
* Stratifies the eval RODs by user-supplied JEXL expressions
|
||||
*
|
||||
* See http://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions for more details
|
||||
* See http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk for more details
|
||||
*/
|
||||
public class JexlExpression extends VariantStratifier implements StandardStratification {
|
||||
// needs to know the jexl expressions
|
||||
|
|
|
|||
|
|
@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
|
|||
import org.broadinstitute.sting.utils.MathUtils;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
import org.broadinstitute.sting.utils.help.HelpUtils;
|
||||
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
|
||||
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
|
@ -80,7 +81,7 @@ public class VariantDataManager {
|
|||
final double theSTD = standardDeviation(theMean, iii);
|
||||
logger.info( annotationKeys.get(iii) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
|
||||
if( Double.isNaN(theMean) ) {
|
||||
throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator");
|
||||
throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See " + HelpUtils.GATK_FORUM_URL + "discussion/49/using-variant-annotator");
|
||||
}
|
||||
|
||||
foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);
|
||||
|
|
|
|||
|
|
@ -51,8 +51,7 @@ import java.util.*;
|
|||
* The Variant Validation Assessor is a tool for vetting/assessing validation data (containing genotypes).
|
||||
* The tool produces a VCF that is annotated with information pertaining to plate quality control and by
|
||||
* default is soft-filtered by high no-call rate or low Hardy-Weinberg probability.
|
||||
* If you have .ped files, please first convert them to VCF format
|
||||
* (see http://www.broadinstitute.org/gsa/wiki/index.php/Converting_ped_to_vcf).
|
||||
* If you have .ped files, please first convert them to VCF format.
|
||||
*
|
||||
* <h2>Input</h2>
|
||||
* <p>
|
||||
|
|
|
|||
|
|
@ -374,7 +374,7 @@ public final class GenomeLocParser {
|
|||
int start = 1;
|
||||
int stop = -1;
|
||||
|
||||
final int colonIndex = str.indexOf(":");
|
||||
final int colonIndex = str.lastIndexOf(":");
|
||||
if(colonIndex == -1) {
|
||||
contig = str.substring(0, str.length()); // chr1
|
||||
stop = Integer.MAX_VALUE;
|
||||
|
|
|
|||
|
|
@ -43,6 +43,9 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
|
|||
// our private storage for the GenomeLoc's
|
||||
private List<GenomeLoc> mArray = new ArrayList<GenomeLoc>();
|
||||
|
||||
// cache this to make overlap checking much more efficient
|
||||
private int previousOverlapSearchIndex = -1;
|
||||
|
||||
/** default constructor */
|
||||
public GenomeLocSortedSet(GenomeLocParser parser) {
|
||||
this.genomeLocParser = parser;
|
||||
|
|
@ -101,7 +104,7 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
|
|||
* Return the number of bps before loc in the sorted set
|
||||
*
|
||||
* @param loc the location before which we are counting bases
|
||||
* @return
|
||||
* @return the number of base pairs over all previous intervals
|
||||
*/
|
||||
public long sizeBeforeLoc(GenomeLoc loc) {
|
||||
long s = 0;
|
||||
|
|
@ -110,7 +113,7 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
|
|||
if ( e.isBefore(loc) )
|
||||
s += e.size();
|
||||
else if ( e.isPast(loc) )
|
||||
; // don't do anything
|
||||
break; // we are done
|
||||
else // loc is inside of s
|
||||
s += loc.getStart() - e.getStart();
|
||||
}
|
||||
|
|
@ -131,15 +134,43 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
|
|||
* Determine if the given loc overlaps any loc in the sorted set
|
||||
*
|
||||
* @param loc the location to test
|
||||
* @return
|
||||
* @return trip if the location overlaps any loc
|
||||
*/
|
||||
public boolean overlaps(final GenomeLoc loc) {
|
||||
for(final GenomeLoc e : mArray) {
|
||||
if(e.overlapsP(loc)) {
|
||||
return true;
|
||||
}
|
||||
// edge condition
|
||||
if ( mArray.isEmpty() )
|
||||
return false;
|
||||
|
||||
// use the cached version first
|
||||
if ( previousOverlapSearchIndex != -1 && overlapsAtOrImmediatelyAfterCachedIndex(loc, true) )
|
||||
return true;
|
||||
|
||||
// update the cached index
|
||||
previousOverlapSearchIndex = Collections.binarySearch(mArray, loc);
|
||||
|
||||
// if it matches an interval exactly, we are done
|
||||
if ( previousOverlapSearchIndex >= 0 )
|
||||
return true;
|
||||
|
||||
// check whether it overlaps the interval before or after the insertion point
|
||||
previousOverlapSearchIndex = Math.max(0, -1 * previousOverlapSearchIndex - 2);
|
||||
return overlapsAtOrImmediatelyAfterCachedIndex(loc, false);
|
||||
}
|
||||
|
||||
private boolean overlapsAtOrImmediatelyAfterCachedIndex(final GenomeLoc loc, final boolean updateCachedIndex) {
|
||||
// check the cached entry
|
||||
if ( mArray.get(previousOverlapSearchIndex).overlapsP(loc) )
|
||||
return true;
|
||||
|
||||
// check the entry after the cached entry since we may have moved to it
|
||||
boolean returnValue = false;
|
||||
if ( previousOverlapSearchIndex < mArray.size() - 1 ) {
|
||||
returnValue = mArray.get(previousOverlapSearchIndex + 1).overlapsP(loc);
|
||||
if ( updateCachedIndex )
|
||||
previousOverlapSearchIndex++;
|
||||
}
|
||||
return false;
|
||||
|
||||
return returnValue;
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -155,7 +186,7 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
|
|||
mArray.add(e);
|
||||
return true;
|
||||
} else {
|
||||
int loc = Collections.binarySearch(mArray,e);
|
||||
final int loc = Collections.binarySearch(mArray,e);
|
||||
if (loc >= 0) {
|
||||
throw new ReviewedStingException("Genome Loc Sorted Set already contains the GenomicLoc " + e.toString());
|
||||
} else {
|
||||
|
|
|
|||
|
|
@ -705,11 +705,13 @@ public class Utils {
|
|||
List<SAMProgramRecord> oldRecords = header.getProgramRecords();
|
||||
List<SAMProgramRecord> newRecords = new ArrayList<SAMProgramRecord>(oldRecords.size()+1);
|
||||
for ( SAMProgramRecord record : oldRecords )
|
||||
if ( !record.getId().startsWith(programRecord.getId()) || KEEP_ALL_PG_RECORDS )
|
||||
if ( (programRecord != null && !record.getId().startsWith(programRecord.getId())) || KEEP_ALL_PG_RECORDS )
|
||||
newRecords.add(record);
|
||||
|
||||
newRecords.add(programRecord);
|
||||
header.setProgramRecords(newRecords);
|
||||
if (programRecord != null) {
|
||||
newRecords.add(programRecord);
|
||||
header.setProgramRecords(newRecords);
|
||||
}
|
||||
return header;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -30,6 +30,7 @@ import net.sf.samtools.SAMSequenceDictionary;
|
|||
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
|
||||
import org.broadinstitute.sting.utils.help.HelpUtils;
|
||||
import org.broadinstitute.sting.utils.sam.ReadUtils;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
|
|
@ -267,7 +268,7 @@ public class UserException extends ReviewedStingException {
|
|||
|
||||
public static class ReadMissingReadGroup extends MalformedBAM {
|
||||
public ReadMissingReadGroup(SAMRecord read) {
|
||||
super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups to fix this problem", read.getReadName()));
|
||||
super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use " + HelpUtils.GATK_FORUM_URL + "discussion/59/companion-utilities-replacereadgroups to fix this problem", read.getReadName()));
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -343,7 +344,7 @@ public class UserException extends ReviewedStingException {
|
|||
super(String.format("Lexicographically sorted human genome sequence detected in %s."
|
||||
+ "\nFor safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs."
|
||||
+ "\nThis is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files."
|
||||
+ "\nYou can use the ReorderSam utility to fix this problem: http://www.broadinstitute.org/gsa/wiki/index.php/ReorderSam"
|
||||
+ "\nYou can use the ReorderSam utility to fix this problem: " + HelpUtils.GATK_FORUM_URL + "discussion/58/companion-utilities-reordersam"
|
||||
+ "\n %s contigs = %s",
|
||||
name, name, ReadUtils.prettyPrintSequenceRecords(dict)));
|
||||
}
|
||||
|
|
|
|||
|
|
@ -44,14 +44,13 @@ public class ForumAPIUtils {
|
|||
/**
|
||||
* How we post to the forum
|
||||
*/
|
||||
private final static String API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
|
||||
final private static String ACCESS_TOKEN = "access_token=";
|
||||
|
||||
public static List<String> getPostedTools(String forumKey) {
|
||||
Gson gson = new Gson();
|
||||
List<String> output = new ArrayList<String>();
|
||||
|
||||
String text = httpGet(API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
|
||||
String text = httpGet(HelpUtils.GATK_FORUM_API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
|
||||
|
||||
APIQuery details = gson.fromJson(text, APIQuery.class);
|
||||
ForumDiscussion[] discussions = details.Discussions;
|
||||
|
|
@ -159,7 +158,7 @@ public class ForumAPIUtils {
|
|||
Gson gson = new Gson();
|
||||
|
||||
String data = gson.toJson(post.getPostData());
|
||||
httpPost(data, API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
|
||||
httpPost(data, HelpUtils.GATK_FORUM_API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -167,8 +166,7 @@ public class ForumAPIUtils {
|
|||
class APIQuery {
|
||||
ForumDiscussion[] Discussions;
|
||||
|
||||
public APIQuery() {
|
||||
}
|
||||
public APIQuery() {}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -28,7 +28,7 @@ public class GATKDocUtils {
|
|||
/**
|
||||
* The URL root for RELEASED GATKDOC units
|
||||
*/
|
||||
public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gatk/gatkdocs/";
|
||||
public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpUtils.GATK_DOCS_URL;
|
||||
/**
|
||||
* The URL root for STABLE GATKDOC units
|
||||
*/
|
||||
|
|
|
|||
|
|
@ -32,6 +32,15 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
|
|||
import java.lang.reflect.Field;
|
||||
|
||||
public class HelpUtils {
|
||||
|
||||
public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk";
|
||||
public final static String GATK_DOCS_URL = BASE_GATK_URL + "/gatkdocs/";
|
||||
public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/";
|
||||
public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
|
||||
|
||||
|
||||
|
||||
|
||||
protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
|
||||
try {
|
||||
Class type = getClassForDoc(classDoc);
|
||||
|
|
|
|||
|
|
@ -71,7 +71,6 @@ abstract class SortingVariantContextWriterBase implements VariantContextWriter {
|
|||
this.takeOwnershipOfInner = takeOwnershipOfInner;
|
||||
|
||||
// has to be PriorityBlockingQueue to be thread-safe
|
||||
// see http://getsatisfaction.com/gsa/topics/missing_loci_output_in_multi_thread_mode_when_implement_sortingvcfwriterbase?utm_content=topic_link&utm_medium=email&utm_source=new_topic
|
||||
this.queue = new PriorityBlockingQueue<VCFRecord>(50, new VariantContextComparator());
|
||||
|
||||
this.mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC;
|
||||
|
|
|
|||
|
|
@ -2,6 +2,8 @@ package org.broadinstitute.sting.utils;
|
|||
|
||||
|
||||
import net.sf.samtools.SAMFileHeader;
|
||||
import net.sf.samtools.SAMSequenceDictionary;
|
||||
import net.sf.samtools.SAMSequenceRecord;
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
|
@ -74,6 +76,23 @@ public class GenomeLocParserUnitTest extends BaseTest {
|
|||
genomeLocParser.parseGenomeLoc("Bad:0-1");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testContigHasColon() {
|
||||
SAMFileHeader header = new SAMFileHeader();
|
||||
header.setSortOrder(net.sf.samtools.SAMFileHeader.SortOrder.coordinate);
|
||||
SAMSequenceDictionary dict = new SAMSequenceDictionary();
|
||||
SAMSequenceRecord rec = new SAMSequenceRecord("c:h:r1", 10);
|
||||
rec.setSequenceLength(10);
|
||||
dict.addSequence(rec);
|
||||
header.setSequenceDictionary(dict);
|
||||
|
||||
final GenomeLocParser myGenomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
|
||||
GenomeLoc loc = myGenomeLocParser.parseGenomeLoc("c:h:r1:4-5");
|
||||
assertEquals(0, loc.getContigIndex());
|
||||
assertEquals(loc.getStart(), 4);
|
||||
assertEquals(loc.getStop(), 5);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testParseGoodString() {
|
||||
GenomeLoc loc = genomeLocParser.parseGenomeLoc("chr1:1-10");
|
||||
|
|
@ -81,7 +100,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
|
|||
assertEquals(loc.getStop(), 10);
|
||||
assertEquals(loc.getStart(), 1);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testCreateGenomeLoc1() {
|
||||
GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 1, 100);
|
||||
|
|
|
|||
|
|
@ -6,6 +6,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
|||
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
|
||||
|
||||
import static org.testng.Assert.assertEquals;
|
||||
import static org.testng.Assert.assertFalse;
|
||||
import static org.testng.Assert.assertTrue;
|
||||
|
||||
import org.testng.annotations.BeforeClass;
|
||||
|
|
@ -117,6 +118,41 @@ public class GenomeLocSortedSetUnitTest extends BaseTest {
|
|||
assertTrue(loc.getContigIndex() == 1);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void overlap() {
|
||||
for ( int i = 1; i < 6; i++ ) {
|
||||
final int start = i * 10;
|
||||
mSortedSet.add(genomeLocParser.createGenomeLoc(contigOneName, start, start + 1));
|
||||
}
|
||||
|
||||
// test matches in and around interval
|
||||
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 9, 9)));
|
||||
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 10, 10)));
|
||||
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 11, 11)));
|
||||
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 12, 12)));
|
||||
|
||||
// test matches spanning intervals
|
||||
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 14, 20)));
|
||||
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 11, 15)));
|
||||
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 30, 40)));
|
||||
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 51, 53)));
|
||||
|
||||
// test miss
|
||||
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 12, 19)));
|
||||
|
||||
// test exact match after miss
|
||||
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 40, 41)));
|
||||
|
||||
// test matches at beginning of intervals
|
||||
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 5, 6)));
|
||||
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 0, 10)));
|
||||
|
||||
// test matches at end of intervals
|
||||
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 52, 53)));
|
||||
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 51, 53)));
|
||||
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 52, 53)));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void mergingOverlappingAbove() {
|
||||
GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 0, 50);
|
||||
|
|
|
|||
|
|
@ -28,7 +28,6 @@ public class VCFIntegrationTest extends WalkerTest {
|
|||
}
|
||||
|
||||
@Test(enabled = true)
|
||||
// See https://getsatisfaction.com/gsa/topics/support_vcf_4_1_structural_variation_breakend_alleles?utm_content=topic_link&utm_medium=email&utm_source=new_topic
|
||||
public void testReadingAndWritingBreakpointAlleles() {
|
||||
String testVCF = privateTestDir + "breakpoint-example.vcf";
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue