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Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Kiran V Garimella 2011-07-26 17:56:48 -04:00
parent 92a11ed8dc 81f8e05bfa
commit 405e521d44
38 changed files with 164 additions and 65 deletions
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2
build.xml
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@ -520,6 +520,8 @@
<fileset dir="${java.classes}">
<include name="**/utils/codecs/**/*.class"/>
<include name="**/utils/variantcontext/**/*.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**"/>
<include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
</fileset>
</jar>
</target>

3
public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
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@ -174,7 +174,8 @@ public class ArgumentDefinitions implements Iterable<ArgumentDefinition> {
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;
}
};
}

2
public/java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java
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@ -44,7 +44,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
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<Integer,List<String>> indices = new TreeMap<Integer,List<String>>();

39
public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
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@ -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<ArgumentDefinition,ArgumentSource> argumentSourcesByDefinition = new HashMap<ArgumentDefinition,ArgumentSource>();
/**
* 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<ArgumentDefinition> argumentsFromSource = new ArrayList<ArgumentDefinition>();
for( ArgumentSource argumentSource: extractArgumentSources(sourceClass) )
argumentsFromSource.addAll( argumentSource.createArgumentDefinitions() );
for( ArgumentSource argumentSource: extractArgumentSources(sourceClass) ) {
List<ArgumentDefinition> 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<ArgumentDefinition> verifiableArguments =
argumentDefinitions.findArgumentDefinitions( null, ArgumentDefinitions.VerifiableDefinitionMatcher );
Collection<Pair<ArgumentDefinition,String>> invalidValues = new ArrayList<Pair<ArgumentDefinition,String>>();
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<ArgumentDefinition,String>(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<ArgumentDefinition,String>(verifiableArgument, value) );
}
}
@ -515,10 +534,14 @@ class InvalidArgumentValueException extends ArgumentException {
private static String formatArguments( Collection<Pair<ArgumentDefinition,String>> invalidArgumentValues ) {
StringBuilder sb = new StringBuilder();
for( Pair<ArgumentDefinition,String> 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();
}

45
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
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@ -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]);
}
}
/**

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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@ -42,7 +42,7 @@ import java.util.List;
import java.util.Map;
public class AlleleBalance implements InfoFieldAnnotation {
public class AlleleBalance extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
Double ratio = annotateSNP(stratifiedContext, vc, g);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java
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@ -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<String, Genotype> genotypes, Map<String, AlignmentContext> stratifiedContexts) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
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@ -46,7 +46,7 @@ import java.util.List;
import java.util.Map;
public class BaseCounts implements InfoFieldAnnotation {
public class BaseCounts extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
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@ -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"),

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
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@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -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";

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -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;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
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@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
double content = computeGCContent(ref);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java
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@ -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;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -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;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
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@ -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;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
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@ -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;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
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@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
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@ -16,7 +16,7 @@ import java.util.List;
import java.util.Map;
public class LowMQ implements InfoFieldAnnotation {
public class LowMQ extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
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@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
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@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref,
AlignmentContext context, VariantContext vc, Genotype g) {
if ( g == null || !g.isCalled() )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
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@ -18,7 +18,7 @@ import java.util.Map;
public class MappingQualityZeroFraction implements InfoFieldAnnotation, ExperimentalAnnotation {
public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
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@ -21,7 +21,7 @@ import java.util.Map;
* Date: 5/16/11
*/
public class NBaseCount implements InfoFieldAnnotation {
public class NBaseCount extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if( stratifiedContexts.size() == 0 )
return null;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
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@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -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;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
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@ -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";

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
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@ -41,7 +41,7 @@ import java.util.List;
import java.util.Map;
public class SampleList implements InfoFieldAnnotation {
public class SampleList extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( vc.isMonomorphic() || !vc.hasGenotypes() )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
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@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
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@ -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";

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
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@ -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";

11
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
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@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g);
// return the FORMAT keys
public List<String> getKeyNames();
public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g);
// return the descriptions used for the VCF FORMAT meta field
public List<VCFFormatHeaderLine> getDescriptions();
public abstract List<VCFFormatHeaderLine> getDescriptions();
}

13
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
View File

@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
// return the INFO keys
public List<String> getKeyNames();
public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
// return the descriptions used for the VCF INFO meta field
public List<VCFInfoHeaderLine> getDescriptions();
public abstract List<VCFInfoHeaderLine> getDescriptions();
}

41
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java 100644
View File

@ -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<String> getKeyNames();
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
View File

@ -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<Difference> diffs = diffEngine.diff(master, test);
diffEngine.reportSummarizedDifferences(diffs, params);
return true;

6
public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
View File

@ -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) ) {

7
public/java/test/org/broadinstitute/sting/MD5DB.java
View File

@ -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);