zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mark DePristo 2011-11-10 11:11:33 -05:00
parent 714cac21c9 0d8983feee
commit 35fe9c8a06
26 changed files with 165 additions and 124 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

48
public/java/src/org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.java
View File

@ -1,48 +0,0 @@
/*
* 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.refdata;
import java.io.File;
/**
* An interface marking that a given Tribble codec can look at the file and determine whether the
* codec specifically parsing the contents of the file.
*/
public interface SelfScopingFeatureCodec {
/**
* This function returns true iff the File potentialInput can be parsed by this
* codec.
*
* The GATK assumes that there's never a situation where two SelfScopingFeaetureCodecs
* return true for the same file. If this occurs the GATK splits out an error.
*
* Note this function must never throw an error. All errors should be trapped
* and false returned.
*
* @param potentialInput the file to test for parsiability with this codec
* @return true if potentialInput can be parsed, false otherwise
*/
public boolean canDecode(final File potentialInput);
}

10
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
View File

@ -30,16 +30,12 @@ import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.NameAwareCodec;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.GATKDocUtils;
import org.broadinstitute.sting.utils.help.HelpUtils;
import javax.mail.Header;
import java.io.File;
import java.util.*;
@ -159,10 +155,8 @@ public class FeatureManager {
public FeatureDescriptor getByFiletype(File file) {
List<FeatureDescriptor> canParse = new ArrayList<FeatureDescriptor>();
for ( FeatureDescriptor descriptor : featureDescriptors )
if ( descriptor.getCodec() instanceof SelfScopingFeatureCodec ) {
if ( ((SelfScopingFeatureCodec) descriptor.getCodec()).canDecode(file) ) {
canParse.add(descriptor);
}
if ( descriptor.getCodec().canDecode(file) ) {
canParse.add(descriptor);
}
if ( canParse.size() == 0 )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
View File

@ -69,7 +69,7 @@ public class AlleleBalance extends InfoFieldAnnotation {
if ( context == null )
continue;
if ( vc.isSNP() ) {
if ( vc.isSNP() && context.hasBasePileup() ) {
final String bases = new String(context.getBasePileup().getBases());
if ( bases.length() == 0 )
return null;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
View File

@ -51,6 +51,9 @@ public class AlleleBalanceBySample extends GenotypeAnnotation implements Experim
if ( altAlleles.size() == 0 )
return null;
if ( !stratifiedContext.hasBasePileup() )
return null;
final String bases = new String(stratifiedContext.getBasePileup().getBases());
if ( bases.length() == 0 )
return null;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
View File

@ -59,6 +59,8 @@ public class BaseCounts extends InfoFieldAnnotation {
int[] counts = new int[4];
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
if ( !sample.getValue().hasBasePileup() )
continue;
for (byte base : sample.getValue().getBasePileup().getBases() ) {
int index = BaseUtils.simpleBaseToBaseIndex(base);
if ( index != -1 )

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
View File

@ -33,18 +33,18 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( mendelianViolation == null ) {
if ( walker instanceof VariantAnnotator ) {
if ( walker instanceof VariantAnnotator && ((VariantAnnotator) walker).familyStr != null) {
mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).familyStr, ((VariantAnnotator)walker).minGenotypeQualityP );
}
else {
throw new UserException("Mendelian violation annotation can only be used from the Variant Annotator");
throw new UserException("Mendelian violation annotation can only be used from the Variant Annotator, and must be provided a valid Family String file (-family) on the command line.");
}
}
Map<String,Object> toRet = new HashMap<String,Object>(1);
boolean hasAppropriateGenotypes = vc.hasGenotype(mendelianViolation.getSampleChild()) &&
vc.hasGenotype(mendelianViolation.getSampleDad()) &&
vc.hasGenotype(mendelianViolation.getSampleMom());
boolean hasAppropriateGenotypes = vc.hasGenotype(mendelianViolation.getSampleChild()) && vc.getGenotype(mendelianViolation.getSampleChild()).hasLikelihoods() &&
vc.hasGenotype(mendelianViolation.getSampleDad()) && vc.getGenotype(mendelianViolation.getSampleDad()).hasLikelihoods() &&
vc.hasGenotype(mendelianViolation.getSampleMom()) && vc.getGenotype(mendelianViolation.getSampleMom()).hasLikelihoods();
if ( hasAppropriateGenotypes )
toRet.put("MVLR",mendelianViolation.violationLikelihoodRatio(vc));

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -33,10 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
@ -180,15 +177,16 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
private void listAnnotationsAndExit() {
System.out.println("\nStandard annotations in the list below are marked with a '*'.");
List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = new PluginManager<InfoFieldAnnotation>(InfoFieldAnnotation.class).getPlugins();
System.out.println("\nAvailable annotations for the VCF INFO field:");
for (int i = 0; i < infoAnnotationClasses.size(); i++)
System.out.println("\t" + infoAnnotationClasses.get(i).getSimpleName());
System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(infoAnnotationClasses.get(i)) ? "*" : "") + infoAnnotationClasses.get(i).getSimpleName());
System.out.println();
List<Class<? extends GenotypeAnnotation>> genotypeAnnotationClasses = new PluginManager<GenotypeAnnotation>(GenotypeAnnotation.class).getPlugins();
System.out.println("\nAvailable annotations for the VCF FORMAT field:");
for (int i = 0; i < genotypeAnnotationClasses.size(); i++)
System.out.println("\t" + genotypeAnnotationClasses.get(i).getSimpleName());
System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(genotypeAnnotationClasses.get(i)) ? "*" : "") + genotypeAnnotationClasses.get(i).getSimpleName());
System.out.println();
System.out.println("\nAvailable classes/groups of annotations:");
for ( Class c : new PluginManager<AnnotationType>(AnnotationType.class).getInterfaces() )

24
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
View File

@ -528,10 +528,10 @@ public class PairHMMIndelErrorModel {
}
else {
byte[] readBases = Arrays.copyOfRange(unclippedReadBases,numStartClippedBases,
final byte[] readBases = Arrays.copyOfRange(unclippedReadBases,numStartClippedBases,
unclippedReadBases.length-numEndClippedBases);
byte[] readQuals = Arrays.copyOfRange(unclippedReadQuals,numStartClippedBases,
final byte[] readQuals = Arrays.copyOfRange(unclippedReadQuals,numStartClippedBases,
unclippedReadBases.length-numEndClippedBases);
int j=0;
@ -540,6 +540,7 @@ public class PairHMMIndelErrorModel {
double[][] matchMetricArray = null, XMetricArray = null, YMetricArray = null;
byte[] previousHaplotypeSeen = null;
double[] previousGOP = null;
double[] previousGCP = null;
int startIdx;
for (Allele a: haplotypeMap.keySet()) {
@ -555,7 +556,7 @@ public class PairHMMIndelErrorModel {
long indStart = start - haplotype.getStartPosition();
long indStop = stop - haplotype.getStartPosition();
byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
final byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
(int)indStart, (int)indStop);
double readLikelihood;
@ -572,13 +573,14 @@ public class PairHMMIndelErrorModel {
if (previousHaplotypeSeen == null)
startIdx = 0;
else {
int s1 = computeFirstDifferingPosition(haplotypeBases, previousHaplotypeSeen);
int s2 = computeFirstDifferingPosition(currentContextGOP, previousGOP);
startIdx = Math.min(s1,s2);
final int s1 = computeFirstDifferingPosition(haplotypeBases, previousHaplotypeSeen);
final int s2 = computeFirstDifferingPosition(currentContextGOP, previousGOP);
final int s3 = computeFirstDifferingPosition(currentContextGCP, previousGCP);
startIdx = Math.min(Math.min(s1, s2), s3);
}
previousHaplotypeSeen = haplotypeBases.clone();
previousGOP = currentContextGOP.clone();
previousGCP = currentContextGCP.clone();
readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals,
@ -617,10 +619,10 @@ public class PairHMMIndelErrorModel {
return 0; // sanity check
for (int i=0; i < b1.length; i++ ){
if ( b1[i]!= b2[i])
if ( b1[i]!= b2[i] )
return i;
}
return 0; // sanity check
return b1.length;
}
private int computeFirstDifferingPosition(double[] b1, double[] b2) {
@ -628,10 +630,10 @@ public class PairHMMIndelErrorModel {
return 0; // sanity check
for (int i=0; i < b1.length; i++ ){
if ( b1[i]!= b2[i])
if ( MathUtils.compareDoubles(b1[i], b2[i]) != 0 )
return i;
}
return 0; // sanity check
return b1.length;
}
private final static double[] getHaplotypeLikelihoods(final int numHaplotypes, final int readCounts[], final double readLikelihoods[][]) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
View File

@ -365,7 +365,7 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
return counter;
// Do not operate on variants that are not covered to the optional minimum depth
if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
if (!context.hasReads() || !context.hasBasePileup() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
counter.nUncovered = 1L;
if (vcComp.getAttribute("GV").equals("T"))
counter.nAltNotCalled = 1L;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
View File

@ -66,6 +66,10 @@ import java.util.*;
* the log odds ratio of being a true variant versus being false under the trained Gaussian mixture model.
*
* <p>
* NOTE: In order to create the model reporting plots Rscript needs to be in your environment PATH (this is the scripting version of R, not the interactive version).
* See <a target="r-project" href="http://www.r-project.org">http://www.r-project.org</a> for more info on how to download and install R.
*
* <p>
* See the GATK wiki for a tutorial and example recalibration accuracy plots.
* http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration
*

6
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -556,9 +556,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
if (vc == null)
return false;
// if we're not looking at specific samples then the absense of a compVC means discordance
if (NO_SAMPLES_SPECIFIED && (compVCs == null || compVCs.isEmpty()))
return true;
// if we're not looking at specific samples then the absence of a compVC means discordance
if (NO_SAMPLES_SPECIFIED)
return (compVCs == null || compVCs.isEmpty());
// check if we find it in the variant rod
Map<String, Genotype> genotypes = vc.getGenotypes(samples);

20
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
View File

@ -58,15 +58,6 @@ public class ReadClipper {
return hardClipByReferenceCoordinates(refStart, -1);
}
private int numDeletions(GATKSAMRecord read) {
int result = 0;
for (CigarElement e: read.getCigar().getCigarElements()) {
if ( e.getOperator() == CigarOperator.DELETION || e.getOperator() == CigarOperator.D )
result =+ e.getLength();
}
return result;
}
protected GATKSAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart, ReadUtils.ClippingTail.RIGHT_TAIL);
int stop = (refStop < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop, ReadUtils.ClippingTail.LEFT_TAIL);
@ -90,7 +81,7 @@ public class ReadClipper {
@Requires("left <= right")
public GATKSAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
if (left == right)
if (read.isEmpty() || left == right)
return new GATKSAMRecord(read.getHeader());
GATKSAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
@ -104,6 +95,9 @@ public class ReadClipper {
}
public GATKSAMRecord hardClipLowQualEnds(byte lowQual) {
if (read.isEmpty())
return read;
byte [] quals = read.getBaseQualities();
int leftClipIndex = 0;
int rightClipIndex = read.getReadLength() - 1;
@ -126,6 +120,9 @@ public class ReadClipper {
}
public GATKSAMRecord hardClipSoftClippedBases () {
if (read.isEmpty())
return read;
int readIndex = 0;
int cutLeft = -1; // first position to hard clip (inclusive)
int cutRight = -1; // first position to hard clip (inclusive)
@ -182,6 +179,9 @@ public class ReadClipper {
}
public GATKSAMRecord hardClipLeadingInsertions() {
if (read.isEmpty())
return read;
for(CigarElement cigarElement : read.getCigar().getCigarElements()) {
if (cigarElement.getOperator() != CigarOperator.HARD_CLIP && cigarElement.getOperator() != CigarOperator.SOFT_CLIP &&
cigarElement.getOperator() != CigarOperator.INSERTION && cigarElement.getOperator() != CigarOperator.DELETION)

2
public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
View File

@ -249,4 +249,6 @@ public class BeagleCodec implements ReferenceDependentFeatureCodec<BeagleFeature
return bglFeature;
}
public boolean canDecode(final File potentialInput) { return false; }
}

4
public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
View File

@ -24,8 +24,8 @@
package org.broadinstitute.sting.utils.codecs.hapmap;
import org.broad.tribble.AbstractFeatureCodec;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.annotation.Strand;
import org.broad.tribble.readers.LineReader;
@ -71,7 +71,7 @@ import java.util.Arrays;
* @author Mark DePristo
* @since 2010
*/
public class RawHapMapCodec implements FeatureCodec {
public class RawHapMapCodec extends AbstractFeatureCodec {
// the minimum number of features in the HapMap file line
private static final int minimumFeatureCount = 11;

4
public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
View File

@ -9,6 +9,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;
import java.util.ArrayList;
/**
@ -138,4 +139,7 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec<RefSeqFeature
public Class<RefSeqFeature> getFeatureType() {
return RefSeqFeature.class;
}
public boolean canDecode(final File potentialInput) { return false; }
}

4
public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java
View File

@ -25,8 +25,8 @@
package org.broadinstitute.sting.utils.codecs.sampileup;
import org.broad.tribble.AbstractFeatureCodec;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.exception.CodecLineParsingException;
import org.broad.tribble.readers.LineReader;
import org.broad.tribble.util.ParsingUtils;
@ -76,7 +76,7 @@ import static org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature.V
* @author Matt Hanna
* @since 2009
*/
public class SAMPileupCodec implements FeatureCodec<SAMPileupFeature> {
public class SAMPileupCodec extends AbstractFeatureCodec<SAMPileupFeature> {
// the number of tokens we expect to parse from a pileup line
private static final int expectedTokenCount = 10;
private static final char fldDelim = '\t';

4
public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java
View File

@ -27,8 +27,8 @@ package org.broadinstitute.sting.utils.codecs.samread;
import net.sf.samtools.Cigar;
import net.sf.samtools.TextCigarCodec;
import net.sf.samtools.util.StringUtil;
import org.broad.tribble.AbstractFeatureCodec;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.exception.CodecLineParsingException;
import org.broad.tribble.readers.LineReader;
import org.broad.tribble.util.ParsingUtils;
@ -52,7 +52,7 @@ import org.broad.tribble.util.ParsingUtils;
* @author Matt Hanna
* @since 2009
*/
public class SAMReadCodec implements FeatureCodec<SAMReadFeature> {
public class SAMReadCodec extends AbstractFeatureCodec<SAMReadFeature> {
/* SL-XBC:1:10:628:923#0 16 Escherichia_coli_K12 1 37 76M = 1 0 AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGA B@>87<;A@?@957:>>@AA@B>@A9AB@B>@A@@@@@A;=AAB@BBBBBCBBBB@>A>:ABB@BAABCB=CA@CB */
// the number of tokens we expect to parse from a read line

10
public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
View File

@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
@ -86,7 +87,13 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
public Object readHeader(LineReader reader) {
String line = "";
try {
boolean isFirst = true;
while ((line = reader.readLine()) != null) {
System.out.println(line);
if ( isFirst && ! line.startsWith(headerDelimiter) && ! line.startsWith(commentDelimiter)) {
throw new UserException.MalformedFile("TableCodec file does not have a header");
}
isFirst &= line.startsWith(commentDelimiter);
if (line.startsWith(headerDelimiter)) {
if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines. The second is = " + line);
String spl[] = line.split(delimiterRegex);
@ -101,4 +108,7 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
}
return header;
}
public boolean canDecode(final File potentialInput) { return false; }
}

6
public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java
View File

@ -1,7 +1,9 @@
package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import java.util.List;
@ -44,6 +46,10 @@ public class TableFeature implements Feature {
return values.get(columnPosition);
}
public String toString() {
return String.format("%s\t%s",position.toString(), Utils.join("\t",values));
}
public String get(String columnName) {
int position = keys.indexOf(columnName);
if (position < 0) throw new IllegalArgumentException("We don't have a column named " + columnName);

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
View File

@ -8,7 +8,6 @@ import org.broad.tribble.TribbleException;
import org.broad.tribble.readers.LineReader;
import org.broad.tribble.util.BlockCompressedInputStream;
import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
@ -20,7 +19,7 @@ import java.util.*;
import java.util.zip.GZIPInputStream;
public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, VCFParser, SelfScopingFeatureCodec {
public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, VCFParser {
protected final static Logger log = Logger.getLogger(VCFCodec.class);
protected final static int NUM_STANDARD_FIELDS = 8; // INFO is the 8th column

80
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -24,7 +24,10 @@
package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.*;
import net.sf.samtools.BAMRecord;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.NGSPlatform;
import java.util.HashMap;
@ -43,7 +46,9 @@ import java.util.Map;
*
*/
public class GATKSAMRecord extends BAMRecord {
public static final String REDUCED_READ_QUALITY_TAG = "RR";
public static final String REDUCED_READ_CONSENSUS_TAG = "RR";
public static final String REDUCED_READ_FILTERED_TAG = "RF";
// the SAMRecord data we're caching
private String mReadString = null;
private GATKSAMReadGroupRecord mReadGroup = null;
@ -83,8 +88,13 @@ public class GATKSAMRecord extends BAMRecord {
read.getMateReferenceIndex(),
read.getMateAlignmentStart(),
read.getInferredInsertSize(),
new byte[]{});
super.clearAttributes();
null);
SAMReadGroupRecord samRG = read.getReadGroup();
clearAttributes();
if (samRG != null) {
GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
setReadGroup(rg);
}
}
public GATKSAMRecord(final SAMFileHeader header,
@ -131,6 +141,21 @@ public class GATKSAMRecord extends BAMRecord {
return mReadGroup;
}
@Override
public int hashCode() {
return super.hashCode();
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (!(o instanceof GATKSAMRecord)) return false;
// note that we do not consider the GATKSAMRecord internal state at all
return super.equals(o);
}
/**
* Efficient caching accessor that returns the GATK NGSPlatform of this read
* @return
@ -142,17 +167,16 @@ public class GATKSAMRecord extends BAMRecord {
public void setReadGroup( final GATKSAMReadGroupRecord readGroup ) {
mReadGroup = readGroup;
retrievedReadGroup = true;
setAttribute("RG", mReadGroup.getId()); // todo -- this should be standardized, but we don't have access to SAMTagUtils!
}
//
//
// Reduced read functions
//
//
///////////////////////////////////////////////////////////////////////////////
// *** ReduceReads functions ***//
///////////////////////////////////////////////////////////////////////////////
public byte[] getReducedReadCounts() {
if ( ! retrievedReduceReadCounts ) {
reducedReadCounts = getByteArrayAttribute(REDUCED_READ_QUALITY_TAG);
reducedReadCounts = getByteArrayAttribute(REDUCED_READ_CONSENSUS_TAG);
retrievedReduceReadCounts = true;
}
@ -167,6 +191,12 @@ public class GATKSAMRecord extends BAMRecord {
return getReducedReadCounts()[i];
}
///////////////////////////////////////////////////////////////////////////////
// *** GATKSAMRecord specific methods ***//
///////////////////////////////////////////////////////////////////////////////
/**
* Checks whether an attribute has been set for the given key.
*
@ -220,18 +250,26 @@ public class GATKSAMRecord extends BAMRecord {
return null;
}
@Override
public int hashCode() {
return super.hashCode();
/**
* Checks whether if the read has any bases.
*
* Empty reads can be dangerous as it may have no cigar strings, no read names and
* other missing attributes.
*
* @return true if the read has no bases
*/
public boolean isEmpty() {
return this.getReadLength() == 0;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (!(o instanceof GATKSAMRecord)) return false;
// note that we do not consider the GATKSAMRecord internal state at all
return super.equals(o);
/**
* Clears all attributes except ReadGroup of the read.
*/
public void simplify () {
GATKSAMReadGroupRecord rg = getReadGroup();
this.clearAttributes();
setReadGroup(rg);
}
}

13
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -64,6 +64,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testDiscordance--" + testFile, spec);
}
@Test
public void testDiscordanceNoSampleSpecified() {
String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s -NO_HEADER",
1,
Arrays.asList("5d7d899c0c4954ec59104aebfe4addd5")
);
executeTest("testDiscordanceNoSampleSpecified--" + testFile, spec);
}
@Test
public void testConcordance() {
String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";

2
public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java
View File

@ -29,7 +29,7 @@ public class ReadUtilsUnitTest extends BaseTest {
reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length());
reducedRead.setReadBases(BASES.getBytes());
reducedRead.setBaseQualityString(QUALS);
reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_QUALITY_TAG, REDUCED_READ_COUNTS);
reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, REDUCED_READ_COUNTS);
}
private void testReadBasesAndQuals(GATKSAMRecord read, int expectedStart, int expectedStop) {

14
public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
View File

@ -162,6 +162,20 @@ public class IntervalIntegrationTest extends WalkerTest {
executeTest("testMixedIntervalMerging", spec);
}
@Test(enabled = true)
public void testBed() {
String md5 = "cf4278314ef8e4b996e1b798d8eb92cf";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T CountLoci" +
" -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
" -R " + hg18Reference +
" -o %s" +
" -L " + validationDataLocation + "intervalTest.bed",
1, // just one output file
Arrays.asList(md5));
executeTest("testBed", spec);
}
@Test(enabled = true)
public void testComplexVCF() {
String md5 = "166d77ac1b46a1ec38aa35ab7e628ab5";

BIN
settings/repository/org.broad/tribble-25.jar → settings/repository/org.broad/tribble-41.jar
View File

Binary file not shown.

2
settings/repository/org.broad/tribble-25.xml → settings/repository/org.broad/tribble-41.xml
View File

@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="25" status="integration" />
<info organisation="org.broad" module="tribble" revision="41" status="integration" />
</ivy-module>