diff --git a/build.xml b/build.xml index fc495f7cc..60c678591 100644 --- a/build.xml +++ b/build.xml @@ -520,6 +520,8 @@ + + diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java index 9f92df6e0..8e3f753a8 100755 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java @@ -174,7 +174,8 @@ public class ArgumentDefinitions implements Iterable { static DefinitionMatcher VerifiableDefinitionMatcher = new DefinitionMatcher() { public boolean matches( ArgumentDefinition definition, Object key ) { - return definition.validation != null; + // We can perform some sort of validation for anything that isn't a flag. + return !definition.isFlag; } }; } diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java index 60ed8c899..351583c07 100755 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java @@ -44,7 +44,7 @@ public class ArgumentMatch implements Iterable { public final String label; /** - * Maps indicies of command line arguments to values paired with that argument. + * Maps indices of command line arguments to values paired with that argument. */ public final SortedMap> indices = new TreeMap>(); diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java index 0dc18e6f9..b7efcd278 100755 --- a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java @@ -41,6 +41,11 @@ import java.util.*; * A parser for Sting command-line arguments. */ public class ParsingEngine { + /** + * The loaded argument sources along with their back definitions. + */ + private Map argumentSourcesByDefinition = new HashMap(); + /** * A list of defined arguments against which command lines are matched. * Package protected for testing access. @@ -107,8 +112,13 @@ public class ParsingEngine { */ public void addArgumentSource( String sourceName, Class sourceClass ) { List argumentsFromSource = new ArrayList(); - for( ArgumentSource argumentSource: extractArgumentSources(sourceClass) ) - argumentsFromSource.addAll( argumentSource.createArgumentDefinitions() ); + for( ArgumentSource argumentSource: extractArgumentSources(sourceClass) ) { + List argumentDefinitions = argumentSource.createArgumentDefinitions(); + for(ArgumentDefinition argumentDefinition: argumentDefinitions) { + argumentSourcesByDefinition.put(argumentDefinition,argumentSource); + argumentsFromSource.add( argumentDefinition ); + } + } argumentDefinitions.add( new ArgumentDefinitionGroup(sourceName, argumentsFromSource) ); } @@ -199,16 +209,25 @@ public class ParsingEngine { throw new InvalidArgumentException( invalidArguments ); } - // Find invalid argument values (arguments that fail the regexp test. + // Find invalid argument values -- invalid arguments are either completely missing or fail the specified 'validation' regular expression. if( !skipValidationOf.contains(ValidationType.InvalidArgumentValue) ) { Collection verifiableArguments = argumentDefinitions.findArgumentDefinitions( null, ArgumentDefinitions.VerifiableDefinitionMatcher ); Collection> invalidValues = new ArrayList>(); for( ArgumentDefinition verifiableArgument: verifiableArguments ) { ArgumentMatches verifiableMatches = argumentMatches.findMatches( verifiableArgument ); + // Check to see whether an argument value was specified. Argument values must be provided + // when the argument name is specified and the argument is not a flag type. + for(ArgumentMatch verifiableMatch: verifiableMatches) { + ArgumentSource argumentSource = argumentSourcesByDefinition.get(verifiableArgument); + if(verifiableMatch.values().size() == 0 && !verifiableArgument.isFlag && argumentSource.createsTypeDefault()) + invalidValues.add(new Pair(verifiableArgument,null)); + } + + // Ensure that the field contents meet the validation criteria specified by the regular expression. for( ArgumentMatch verifiableMatch: verifiableMatches ) { for( String value: verifiableMatch.values() ) { - if( !value.matches(verifiableArgument.validation) ) + if( verifiableArgument.validation != null && !value.matches(verifiableArgument.validation) ) invalidValues.add( new Pair(verifiableArgument, value) ); } } @@ -515,10 +534,14 @@ class InvalidArgumentValueException extends ArgumentException { private static String formatArguments( Collection> invalidArgumentValues ) { StringBuilder sb = new StringBuilder(); for( Pair invalidValue: invalidArgumentValues ) { - sb.append( String.format("%nArgument '--%s' has value of incorrect format: %s (should match %s)", - invalidValue.first.fullName, - invalidValue.second, - invalidValue.first.validation) ); + if(invalidValue.getSecond() == null) + sb.append( String.format("%nArgument '--%s' requires a value but none was provided", + invalidValue.first.fullName) ); + else + sb.append( String.format("%nArgument '--%s' has value of incorrect format: %s (should match %s)", + invalidValue.first.fullName, + invalidValue.second, + invalidValue.first.validation) ); } return sb.toString(); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java index 6064806f3..572970349 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java @@ -893,6 +893,7 @@ public class SAMDataSource { * Custom representation of interval bounds. * Makes it simpler to track current position. */ + private int[] intervalContigIndices; private int[] intervalStarts; private int[] intervalEnds; @@ -917,12 +918,14 @@ public class SAMDataSource { if(foundMappedIntervals) { if(keepOnlyUnmappedReads) throw new ReviewedStingException("Tried to apply IntervalOverlapFilteringIterator to a mixed of mapped and unmapped intervals. Please apply this filter to only mapped or only unmapped reads"); + this.intervalContigIndices = new int[intervals.size()]; this.intervalStarts = new int[intervals.size()]; this.intervalEnds = new int[intervals.size()]; int i = 0; for(GenomeLoc interval: intervals) { - intervalStarts[i] = (int)interval.getStart(); - intervalEnds[i] = (int)interval.getStop(); + intervalContigIndices[i] = interval.getContigIndex(); + intervalStarts[i] = interval.getStart(); + intervalEnds[i] = interval.getStop(); i++; } } @@ -961,11 +964,10 @@ public class SAMDataSource { while(nextRead == null && (keepOnlyUnmappedReads || currentBound < intervalStarts.length)) { if(!keepOnlyUnmappedReads) { // Mapped read filter; check against GenomeLoc-derived bounds. - if(candidateRead.getAlignmentEnd() >= intervalStarts[currentBound] || - (candidateRead.getReadUnmappedFlag() && candidateRead.getAlignmentStart() >= intervalStarts[currentBound])) { - // This read ends after the current interval begins (or, if unmapped, starts within the bounds of the interval. + if(readEndsOnOrAfterStartingBound(candidateRead)) { + // This read ends after the current interval begins. // Promising, but this read must be checked against the ending bound. - if(candidateRead.getAlignmentStart() <= intervalEnds[currentBound]) { + if(readStartsOnOrBeforeEndingBound(candidateRead)) { // Yes, this read is within both bounds. This must be our next read. nextRead = candidateRead; break; @@ -993,6 +995,37 @@ public class SAMDataSource { candidateRead = iterator.next(); } } + + /** + * Check whether the read lies after the start of the current bound. If the read is unmapped but placed, its + * end will be distorted, so rely only on the alignment start. + * @param read The read to position-check. + * @return True if the read starts after the current bounds. False otherwise. + */ + private boolean readEndsOnOrAfterStartingBound(final SAMRecord read) { + return + // Read ends on a later contig, or... + read.getReferenceIndex() > intervalContigIndices[currentBound] || + // Read ends of this contig... + (read.getReferenceIndex() == intervalContigIndices[currentBound] && + // either after this location, or... + (read.getAlignmentEnd() >= intervalStarts[currentBound] || + // read is unmapped but positioned and alignment start is on or after this start point. + (read.getReadUnmappedFlag() && read.getAlignmentStart() >= intervalStarts[currentBound]))); + } + + /** + * Check whether the read lies before the end of the current bound. + * @param read The read to position-check. + * @return True if the read starts after the current bounds. False otherwise. + */ + private boolean readStartsOnOrBeforeEndingBound(final SAMRecord read) { + return + // Read starts on a prior contig, or... + read.getReferenceIndex() < intervalContigIndices[currentBound] || + // Read starts on this contig and the alignment start is registered before this end point. + (read.getReferenceIndex() == intervalContigIndices[currentBound] && read.getAlignmentStart() <= intervalEnds[currentBound]); + } } /** 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 3144098a8..784927ab4 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 @@ -42,7 +42,7 @@ import java.util.List; import java.util.Map; -public class AlleleBalance implements InfoFieldAnnotation { +public class AlleleBalance extends InfoFieldAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) 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 a99f87a70..f70a87dc5 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 @@ -15,7 +15,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; -public class AlleleBalanceBySample implements GenotypeAnnotation, ExperimentalAnnotation { +public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) { Double ratio = annotateSNP(stratifiedContext, vc, g); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java index 6c14e7445..dc41dbc81 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java @@ -8,7 +8,7 @@ import java.util.Map; -public abstract class AnnotationByDepth implements InfoFieldAnnotation { +public abstract class AnnotationByDepth extends InfoFieldAnnotation { protected int annotationByVariantDepth(final Map genotypes, Map stratifiedContexts) { 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 66416ce11..7cd159c5d 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 @@ -46,7 +46,7 @@ import java.util.List; import java.util.Map; -public class BaseCounts implements InfoFieldAnnotation { +public class BaseCounts extends InfoFieldAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) 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 74f7f9d80..9b30079d0 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 @@ -43,7 +43,7 @@ import java.util.List; import java.util.Map; -public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation { +public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation { private String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY }; private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"), 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 c384e0d09..d8907c57f 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 @@ -16,7 +16,7 @@ import java.util.List; import java.util.Map; -public class DepthOfCoverage implements InfoFieldAnnotation, StandardAnnotation { +public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) 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 e3e8bc258..20513421d 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 @@ -22,7 +22,7 @@ import java.util.List; import java.util.Map; -public class DepthPerAlleleBySample implements GenotypeAnnotation, StandardAnnotation { +public class DepthPerAlleleBySample extends GenotypeAnnotation implements StandardAnnotation { private static String REF_ALLELE = "REF"; 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 97ed221e7..e71febece 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 @@ -42,7 +42,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; -public class FisherStrand implements InfoFieldAnnotation, StandardAnnotation { +public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation { private static final String FS = "FS"; private static final double MIN_PVALUE = 1E-320; 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 48677bbe5..588d3e98a 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 @@ -16,7 +16,7 @@ import java.util.List; import java.util.Map; -public class GCContent implements InfoFieldAnnotation, ExperimentalAnnotation { +public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { double content = computeGCContent(ref); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java index cca0ad4bc..862e12f7d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java @@ -23,7 +23,7 @@ import java.util.Map; */ // A set of annotations calculated directly from the GLs -public class GLstats implements InfoFieldAnnotation, StandardAnnotation { +public class GLstats extends InfoFieldAnnotation implements StandardAnnotation { private static final int MIN_SAMPLES = 10; 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 b175579f1..2196de389 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 @@ -48,7 +48,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; -public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation { +public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnotation { private final static boolean DEBUG = false; private final static int MIN_CONTEXT_WING_SIZE = 10; private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 50; 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 d86728d5e..2d9424e98 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 @@ -18,7 +18,7 @@ import java.util.List; import java.util.Map; -public class HardyWeinberg implements InfoFieldAnnotation, WorkInProgressAnnotation { +public class HardyWeinberg extends InfoFieldAnnotation implements WorkInProgressAnnotation { private static final int MIN_SAMPLES = 10; private static final int MIN_GENOTYPE_QUALITY = 10; 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 02efd854c..870e9992b 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 @@ -16,7 +16,7 @@ import java.util.List; import java.util.Map; -public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation { +public class HomopolymerRun extends InfoFieldAnnotation implements StandardAnnotation { private boolean ANNOTATE_INDELS = true; 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 2fd62ddf3..b1c16ba0d 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 @@ -19,7 +19,7 @@ import java.util.*; * Time: 11:47:33 AM * To change this template use File | Settings | File Templates. */ -public class IndelType implements InfoFieldAnnotation, ExperimentalAnnotation { +public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { 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 1d999c531..5de9aaa3b 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 @@ -16,7 +16,7 @@ import java.util.List; import java.util.Map; -public class LowMQ implements InfoFieldAnnotation { +public class LowMQ extends InfoFieldAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) 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 f240d02bc..60bfe945f 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 @@ -18,7 +18,7 @@ import java.util.List; import java.util.Map; -public class MappingQualityZero implements InfoFieldAnnotation, StandardAnnotation { +public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) 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 0ca53adf2..f2b7b72b9 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 @@ -49,7 +49,7 @@ import java.util.Map; * Time: 6:46:25 PM * To change this template use File | Settings | File Templates. */ -public class MappingQualityZeroBySample implements GenotypeAnnotation { +public class MappingQualityZeroBySample extends GenotypeAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantContext vc, Genotype g) { if ( g == null || !g.isCalled() ) 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 08a25a7e3..3a6c9dce9 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 @@ -18,7 +18,7 @@ import java.util.Map; -public class MappingQualityZeroFraction implements InfoFieldAnnotation, ExperimentalAnnotation { +public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) 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 1c70a1b33..9f67acf65 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 @@ -21,7 +21,7 @@ import java.util.Map; * Date: 5/16/11 */ -public class NBaseCount implements InfoFieldAnnotation { +public class NBaseCount extends InfoFieldAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if( stratifiedContexts.size() == 0 ) return null; 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 2175d39e6..20bee9008 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 @@ -16,7 +16,7 @@ import java.util.List; import java.util.Map; -public class QualByDepth extends AnnotationByDepth implements InfoFieldAnnotation, StandardAnnotation { +public class QualByDepth extends AnnotationByDepth implements StandardAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) 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 d52f07b58..d1d9871e7 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 @@ -20,7 +20,7 @@ import java.util.List; import java.util.Map; -public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotation { +public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) 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 5466828f6..643056c1d 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 @@ -21,7 +21,7 @@ import java.util.Map; -public abstract class RankSumTest implements InfoFieldAnnotation, StandardAnnotation { +public abstract class RankSumTest extends InfoFieldAnnotation implements StandardAnnotation { static final double INDEL_LIKELIHOOD_THRESH = 0.1; static final boolean DEBUG = false; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java index c56e2622d..f3e99235a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java @@ -52,7 +52,7 @@ import java.util.Map; * Time: 3:59:27 PM * To change this template use File | Settings | File Templates. */ -public class ReadDepthAndAllelicFractionBySample implements GenotypeAnnotation { +public class ReadDepthAndAllelicFractionBySample extends GenotypeAnnotation { private static String REF_ALLELE = "REF"; 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 ff9092a71..3712ca8ae 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 @@ -41,7 +41,7 @@ import java.util.List; import java.util.Map; -public class SampleList implements InfoFieldAnnotation { +public class SampleList extends InfoFieldAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( vc.isMonomorphic() || !vc.hasGenotypes() ) 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 a4668eeb6..332b0226b 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 @@ -16,7 +16,7 @@ import java.util.List; import java.util.Map; -public class SpanningDeletions implements InfoFieldAnnotation, StandardAnnotation { +public class SpanningDeletions extends InfoFieldAnnotation implements StandardAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) 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 b46d82d8b..626142cd2 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 @@ -24,7 +24,7 @@ import java.util.Map; * Time: 3:14 PM * To change this template use File | Settings | File Templates. */ -public class TechnologyComposition implements ExperimentalAnnotation,InfoFieldAnnotation { +public class TechnologyComposition extends InfoFieldAnnotation implements ExperimentalAnnotation { private String nSLX = "NumSLX"; private String n454 ="Num454"; private String nSolid = "NumSOLiD"; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java index 05c1b3c52..0e8360484 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java @@ -48,7 +48,7 @@ import java.util.Map.Entry; * * For details, see: http://www.broadinstitute.org/gsa/wiki/index.php/GenomicAnnotator */ -public class GenomicAnnotation implements InfoFieldAnnotation { +public class GenomicAnnotation extends InfoFieldAnnotation { public static final String CHR_COLUMN = "chr"; public static final String START_COLUMN = "start"; 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 57bc44ab8..e982582ee 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 @@ -10,15 +10,12 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.List; import java.util.Map; -public interface GenotypeAnnotation { +public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation { // return annotations for the given contexts/genotype split by sample - public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g); - - // return the FORMAT keys - public List getKeyNames(); + public abstract Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g); // return the descriptions used for the VCF FORMAT meta field - public List getDescriptions(); - + public abstract List getDescriptions(); + } \ No newline at end of file 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 4e850d01b..84438ccd8 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 @@ -3,21 +3,18 @@ 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.annotator.VariantAnnotator; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.List; import java.util.Map; -public interface InfoFieldAnnotation { - +public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation { // return annotations for the given contexts split by sample - public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc); - - // return the INFO keys - public List getKeyNames(); + public abstract Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc); // return the descriptions used for the VCF INFO meta field - public List getDescriptions(); - + public abstract List getDescriptions(); } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java new file mode 100644 index 000000000..f33d61df9 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java @@ -0,0 +1,41 @@ +/* + * 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.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.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.util.List; +import java.util.Map; + +@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations") +public abstract class VariantAnnotatorAnnotation { + // return the INFO keys + public abstract List getKeyNames(); +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java index 5f8f19892..4a4f6f6af 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java @@ -342,12 +342,12 @@ public class DiffEngine { return reader.readFromFile(file, maxElementsToRead); } - public static boolean simpleDiffFiles(File masterFile, File testFile, DiffEngine.SummaryReportParams params) { + public static boolean simpleDiffFiles(File masterFile, File testFile, int maxElementsToRead, DiffEngine.SummaryReportParams params) { DiffEngine diffEngine = new DiffEngine(); if ( diffEngine.canRead(masterFile) && diffEngine.canRead(testFile) ) { - DiffElement master = diffEngine.createDiffableFromFile(masterFile); - DiffElement test = diffEngine.createDiffableFromFile(testFile); + DiffElement master = diffEngine.createDiffableFromFile(masterFile, maxElementsToRead); + DiffElement test = diffEngine.createDiffableFromFile(testFile, maxElementsToRead); List diffs = diffEngine.diff(master, test); diffEngine.reportSummarizedDifferences(diffs, params); return true; diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java index 0b4c69e3c..49214237a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java @@ -57,7 +57,7 @@ public class GATKDoclet { * @throws java.io.IOException if output can't be written. */ public static boolean start(RootDoc rootDoc) throws IOException { - logger.setLevel(Level.INFO); + logger.setLevel(Level.DEBUG); // load arguments for(String[] options: rootDoc.options()) { if(options[0].equals("-build-timestamp")) @@ -95,6 +95,10 @@ public class GATKDoclet { for ( ClassDoc doc : rootDoc.classes() ) { logger.debug("Considering " + doc); Class clazz = getClassForClassDoc(doc); + + if ( clazz != null && clazz.getName().equals("org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance")) + logger.debug("foo"); + DocumentedGATKFeature feature = getFeatureForClassDoc(doc); DocumentedGATKFeatureHandler handler = createHandler(doc, feature); if ( handler != null && handler.shouldBeProcessed(doc) ) { diff --git a/public/java/test/org/broadinstitute/sting/MD5DB.java b/public/java/test/org/broadinstitute/sting/MD5DB.java index bea9eaec5..0194e114a 100644 --- a/public/java/test/org/broadinstitute/sting/MD5DB.java +++ b/public/java/test/org/broadinstitute/sting/MD5DB.java @@ -47,6 +47,7 @@ public class MD5DB { /** * Subdirectory under the ant build directory where we store integration test md5 results */ + private static final int MAX_RECORDS_TO_READ = 10000; public static final String LOCAL_MD5_DB_DIR = "integrationtests"; public static final String GLOBAL_MD5_DB_DIR = "/humgen/gsa-hpprojects/GATK/data/integrationtests"; @@ -78,8 +79,8 @@ public class MD5DB { * @return */ public static String getMD5FilePath(final String md5, final String valueIfNotFound) { - // we prefer the local db to the global DB, so match it first - for ( String dir : Arrays.asList(LOCAL_MD5_DB_DIR, GLOBAL_MD5_DB_DIR)) { + // we prefer the global db to the local DB, so match it first + for ( String dir : Arrays.asList(GLOBAL_MD5_DB_DIR, LOCAL_MD5_DB_DIR)) { File f = getFileForMD5(md5, dir); if ( f.exists() && f.canRead() ) return f.getPath(); @@ -232,7 +233,7 @@ public class MD5DB { // inline differences DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(System.out, 20, 10, 0); - boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), params); + boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), MAX_RECORDS_TO_READ, params); if ( success ) System.out.printf("Note that the above list is not comprehensive. At most 20 lines of output, and 10 specific differences will be listed. Please use -T DiffObjects -R public/testdata/exampleFASTA.fasta -m %s -t %s to explore the differences more freely%n", pathToExpectedMD5File, pathToFileMD5File);