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Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3397 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-05-19 23:27:55 +00:00
parent 02cc1afdc8
commit 8a725b6c93
97 changed files with 398 additions and 266 deletions
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11
java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.alignment;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.commandline.Argument;
@ -69,14 +70,6 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
aligner = new BWACAligner(bwtFiles,configuration);
}
/** Must return true for reads that need to be processed. Reads, for which this method return false will
* be skipped by the engine and never passed to the walker.
*/
@Override
public boolean filter(char[] ref, SAMRecord read) {
return true;
}
/**
* Aligns a read to the given reference.
* @param ref Reference over the read. Read will most likely be unmapped, so ref will be null.
@ -84,7 +77,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
* @return Number of reads aligned by this map (aka 1).
*/
@Override
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
//logger.info(String.format("examining read %s", read.getReadName()));
byte[] bases = read.getReadBases();

11
java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
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@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.BWTFiles;
@ -70,14 +71,6 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
*/
private SAMFileHeader header;
/** Must return true for reads that need to be processed. Reads, for which this method return false will
* be skipped by the engine and never passed to the walker.
*/
@Override
public boolean filter(char[] ref, SAMRecord read) {
return true;
}
/**
* Create an aligner object. The aligner object will load and hold the BWT until close() is called.
*/
@ -109,7 +102,7 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
* @return Number of alignments found for this read.
*/
@Override
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
SAMRecord alignedRead = aligner.align(read,header);
if (outputBam != null) {
outputBam.addAlignment(alignedRead);

3
java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.alignment;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.alignment.bwa.BWTFiles;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
@ -75,7 +76,7 @@ public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
* @return Number of alignments found for this read.
*/
@Override
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
Iterator<Alignment[]> alignmentIterator = aligner.getAllAlignments(read.getReadBases()).iterator();
if(alignmentIterator.hasNext()) {
int numAlignments = alignmentIterator.next().length;

36
java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
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@ -51,18 +51,20 @@ public class ReferenceContext {
/**
* The bases in the window around the current locus.
*/
private char[] bases;
private byte[] bases;
private char[] basesAsCharCached = null;
/**
* Contructor for a simple, windowless reference context.
* @param locus locus of interest.
* @param base reference base at that locus.
*/
public ReferenceContext( GenomeLoc locus, char base ) {
this( locus, locus, new char[] { base } );
public ReferenceContext( GenomeLoc locus, byte base ) {
this( locus, locus, new byte[] { base } );
}
public ReferenceContext( GenomeLoc locus, GenomeLoc window, char[] bases ) {
public ReferenceContext( GenomeLoc locus, GenomeLoc window, byte[] bases ) {
// if( !window.containsP(locus) )
// throw new StingException("Invalid locus or window; window does not contain locus");
@ -87,10 +89,15 @@ public class ReferenceContext {
* Get the base at the given locus.
* @return The base at the given locus from the reference.
*/
public char getBase() {
public byte getBase() {
return bases[(int)(locus.getStart() - window.getStart())];
}
@Deprecated
public char getBaseAsChar() {
return (char)getBase();
}
/**
* Get the base at the given locus.
* @return The base at the given locus from the reference.
@ -104,10 +111,18 @@ public class ReferenceContext {
* @return All bases available. If the window is of size [0,0], the array will
* contain only the base at the given locus.
*/
public char[] getBases() {
public byte[] getBases() {
return bases;
}
@Deprecated
public char[] getBasesAsChars() {
if ( basesAsCharCached == null )
basesAsCharCached = new String(bases).toCharArray();
return basesAsCharCached;
}
/** Extracts from the current window and returns n bases starting at this context's locus (NOT
* from the window start!). The returned array of chars is newly allocated. If n is too large (runs beyond
* the right boundary of this context's window), an exception will be thrown. If n==(-1), all bases starting
@ -115,12 +130,12 @@ public class ReferenceContext {
* @param n number of requested bases including and starting from the current locus
* @return
*/
public char[] getBasesAtLocus(int n) {
public byte[] getBasesAtLocusAsByte(int n) {
int start = (int)(locus.getStart()-window.getStart());
int stop = ( n==(-1) ? bases.length : start+n );
char[] b = new char[stop-start];
byte[] b = new byte[stop-start];
if ( stop > bases.length )
throw new StingException("Bases beyond the current window requested: window="+window+", requested="+n);
@ -129,4 +144,9 @@ public class ReferenceContext {
for ( int j = start ; j < stop ; j++) b[i++]=bases[j];
return b;
}
@Deprecated
public char[] getBasesAtLocus(int n) {
return new String(getBasesAtLocusAsByte(n)).toCharArray();
}
}

11
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Allele.java
View File

@ -120,6 +120,16 @@ public class Allele implements Comparable<Allele> {
throw new IllegalArgumentException("Unexpected base in allele bases " + new String(bases));
}
public Allele(byte base, boolean isRef) {
this( base1ToBases(base), isRef);
}
private static byte[] base1ToBases(byte base) {
byte[] bases = { base };
return bases;
}
/**
* @param bases bases representing an allele
* @return true if the bases represent the null allele
@ -171,6 +181,7 @@ public class Allele implements Comparable<Allele> {
this(bases.getBytes(), isRef);
}
/**
* Creates a non-Ref allele. @see Allele(byte[], boolean) for full information
*

34
java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
View File

@ -174,27 +174,51 @@ public class LocusReferenceView extends ReferenceView {
//validateLocation( genomeLoc );
GenomeLoc window = GenomeLocParser.createGenomeLoc( genomeLoc.getContig(), getWindowStart(genomeLoc), getWindowStop(genomeLoc) );
char[] bases = null;
if(bounds != null) {
int refStart = -1;
if (bounds != null) {
window = trimToBounds(window);
bases = StringUtil.bytesToString( referenceSequence.getBases(), (int)(window.getStart() - getWindowStart(bounds)), (int)window.size() ).toCharArray();
refStart = (int)(window.getStart() - getWindowStart(bounds));
}
else {
if(referenceSequence == null || referenceSequence.getContigIndex() != genomeLoc.getContigIndex())
referenceSequence = reference.getSequence(genomeLoc.getContig());
bases = StringUtil.bytesToString( referenceSequence.getBases(), (int)window.getStart()-1, (int)window.size()).toCharArray();
refStart = (int)window.getStart()-1;
}
// todo -- how often is this copy unnecessary?
int len = (int)window.size();
byte[] bases = new byte[len];
System.arraycopy(referenceSequence.getBases(), refStart, bases, 0, len);
return new ReferenceContext( genomeLoc, window, bases );
}
// public ReferenceContext getReferenceContext( GenomeLoc genomeLoc ) {
// //validateLocation( genomeLoc );
//
// GenomeLoc window = GenomeLocParser.createGenomeLoc( genomeLoc.getContig(), getWindowStart(genomeLoc), getWindowStop(genomeLoc) );
// char[] bases = null;
//
// if(bounds != null) {
// window = trimToBounds(window);
// bases = StringUtil.bytesToString( referenceSequence.getBases(), (int)(window.getStart() - getWindowStart(bounds)), (int)window.size() ).toCharArray();
// }
// else {
// if(referenceSequence == null || referenceSequence.getContigIndex() != genomeLoc.getContigIndex())
// referenceSequence = reference.getSequence(genomeLoc.getContig());
// bases = StringUtil.bytesToString( referenceSequence.getBases(), (int)window.getStart()-1, (int)window.size()).toCharArray();
// }
// return new ReferenceContext( genomeLoc, window, bases );
// }
/**
* Allow the user to pull reference info from any arbitrary region of the reference.
* @param genomeLoc The locus.
* @return A list of the bases starting at the start of the locus (inclusive) and ending
* at the end of the locus (inclusive).
*/
public char[] getReferenceBases( GenomeLoc genomeLoc ) {
public byte[] getReferenceBases( GenomeLoc genomeLoc ) {
return super.getReferenceBases(genomeLoc);
}

15
java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
View File

@ -7,6 +7,7 @@ import net.sf.picard.reference.ReferenceSequence;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
/*
* Copyright (c) 2009 The Broad Institute
*
@ -61,10 +62,16 @@ public class ReadReferenceView extends ReferenceView {
* mapped to the reference, followed by X's coresponding to the rest of the read.
* This indicates that the rest lies off the end of the contig.
*/
public char[] getReferenceBases( SAMRecord read ) {
if (read.getReadUnmappedFlag())
return null;
return getReferenceBases( GenomeLocParser.createGenomeLoc(read) );
// public char[] getReferenceBases( SAMRecord read ) {
// if (read.getReadUnmappedFlag())
// return null;
// return getReferenceBases( GenomeLocParser.createGenomeLoc(read) );
// }
public ReferenceContext getReferenceContext( SAMRecord read ) {
GenomeLoc loc = GenomeLocParser.createGenomeLoc(read);
byte[] bases = super.getReferenceBases(loc);
return new ReferenceContext( loc, loc, bases );
}
}

41
java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
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@ -3,11 +3,15 @@ package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.Collections;
import java.util.Collection;
import java.util.Arrays;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.StringUtil;
import net.sf.picard.reference.ReferenceSequence;
/**
@ -60,10 +64,41 @@ public class ReferenceView implements View {
* @return A list of the bases starting at the start of the locus (inclusive) and ending
* at the end of the locus (inclusive).
*/
protected char[] getReferenceBases( GenomeLoc genomeLoc ) {
// protected char[] getReferenceBasesAsChars( GenomeLoc genomeLoc ) {
//// SAMSequenceRecord sequenceInfo = reference.getSequenceDictionary().getSequence(genomeLoc.getContig());
//// long stop = Math.min( genomeLoc.getStop(), sequenceInfo.getSequenceLength() );
//// ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(),genomeLoc.getStart(),stop);
//// return (StringUtil.bytesToString(subsequence.getBases()) + Utils.dupString('X', (int)(genomeLoc.getStop() - stop)) ).toCharArray();
// return new String(getReferenceBases(genomeLoc)).toCharArray();
// }
final static int BUFFER = 10000;
final static byte[] Xs = new byte[BUFFER];
static {
Arrays.fill(Xs, (byte)'X');
}
protected byte[] getReferenceBases( SAMRecord read ) {
return getReferenceBases(GenomeLocParser.createGenomeLoc(read));
}
protected byte[] getReferenceBases( GenomeLoc genomeLoc ) {
SAMSequenceRecord sequenceInfo = reference.getSequenceDictionary().getSequence(genomeLoc.getContig());
long stop = Math.min( genomeLoc.getStop(), sequenceInfo.getSequenceLength() );
ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(),genomeLoc.getStart(),stop);
return (StringUtil.bytesToString(subsequence.getBases()) + Utils.dupString('X', (int)(genomeLoc.getStop() - stop)) ).toCharArray();
ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(), genomeLoc.getStart(), stop);
int overhang = (int)(genomeLoc.getStop() - stop);
if ( overhang > 0 ) {
if ( overhang > BUFFER ) // todo -- this is a bit dangerous
throw new StingException("Insufficient buffer size for Xs overhanging genome -- expand BUFFER");
byte[] all = new byte[subsequence.getBases().length + overhang];
System.arraycopy(subsequence.getBases(), 0, all, 0, subsequence.getBases().length);
System.arraycopy(Xs, 0, all, subsequence.getBases().length, overhang);
return all;
} else {
// fast path
return subsequence.getBases();
}
}
}

17
java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
View File

@ -232,6 +232,7 @@ public class RefMetaDataTracker {
*
* see getVariantContexts for more information.
*
* @param ref ReferenceContext to enable conversion to variant context
* @param name name
* @param curLocation location
* @param allowedTypes allowed types
@ -239,17 +240,17 @@ public class RefMetaDataTracker {
* @param takeFirstOnly do we take the first rod only?
* @return variant context
*/
public Collection<VariantContext> getVariantContexts(String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
return getVariantContexts(null, Arrays.asList(name), allowedTypes, curLocation, requireStartHere, takeFirstOnly);
}
// public Collection<VariantContext> getVariantContexts(String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
// return getVariantContexts(null, Arrays.asList(name), allowedTypes, curLocation, requireStartHere, takeFirstOnly);
// }
public Collection<VariantContext> getVariantContexts(ReferenceContext ref, String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
return getVariantContexts(ref, Arrays.asList(name), allowedTypes, curLocation, requireStartHere, takeFirstOnly);
}
public Collection<VariantContext> getVariantContexts(Collection<String> names, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
return getVariantContexts(null, names, allowedTypes, curLocation, requireStartHere, takeFirstOnly);
}
// public Collection<VariantContext> getVariantContexts(Collection<String> names, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
// return getVariantContexts(null, names, allowedTypes, curLocation, requireStartHere, takeFirstOnly);
// }
public Collection<VariantContext> getVariantContexts(ReferenceContext ref, Collection<String> names, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
Collection<VariantContext> contexts = new ArrayList<VariantContext>();
@ -274,8 +275,8 @@ public class RefMetaDataTracker {
* @param requireStartHere do we require the rod to start at this location?
* @return variant context
*/
public VariantContext getVariantContext(String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere ) {
Collection<VariantContext> contexts = getVariantContexts(name, allowedTypes, curLocation, requireStartHere, false );
public VariantContext getVariantContext(ReferenceContext ref, String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere ) {
Collection<VariantContext> contexts = getVariantContexts(ref, name, allowedTypes, curLocation, requireStartHere, false );
if ( contexts.size() > 1 )
throw new StingException("Requested a single VariantContext object for track " + name + " but multiple variants were present at position " + curLocation);

99
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
View File

@ -61,17 +61,17 @@ public class VariantContextAdaptors {
/** generic superclass */
private static abstract class VCAdaptor {
abstract VariantContext convert(String name, Object input);
// abstract VariantContext convert(String name, Object input);
abstract VariantContext convert(String name, Object input, ReferenceContext ref);
}
public static VariantContext toVariantContext(String name, Object variantContainingObject) {
if ( ! adaptors.containsKey(variantContainingObject.getClass()) )
return null;
else {
return adaptors.get(variantContainingObject.getClass()).convert(name, variantContainingObject);
}
}
// public static VariantContext toVariantContext(String name, Object variantContainingObject) {
// if ( ! adaptors.containsKey(variantContainingObject.getClass()) )
// return null;
// else {
// return adaptors.get(variantContainingObject.getClass()).convert(name, variantContainingObject);
// }
// }
public static VariantContext toVariantContext(String name, Object variantContainingObject, ReferenceContext ref) {
if ( ! adaptors.containsKey(variantContainingObject.getClass()) )
@ -96,9 +96,9 @@ public class VariantContextAdaptors {
// --------------------------------------------------------------------------------------------------------------
private static class DBSnpAdaptor extends VCAdaptor {
VariantContext convert(String name, Object input) {
return convert(name, input, null);
}
// VariantContext convert(String name, Object input) {
// return convert(name, input, null);
// }
VariantContext convert(String name, Object input, ReferenceContext ref) {
DbSNPFeature dbsnp = (DbSNPFeature)input;
@ -132,10 +132,10 @@ public class VariantContextAdaptors {
}
private static class VCFRecordAdaptor extends VCAdaptor {
// WARNING: do not use this method if you have anything other than point mutations in your VCF
VariantContext convert(String name, Object input) {
return vcfToVariantContext(name, (VCFRecord)input, null);
}
// // WARNING: do not use this method if you have anything other than point mutations in your VCF
// VariantContext convert(String name, Object input) {
// return vcfToVariantContext(name, (VCFRecord)input, null);
// }
VariantContext convert(String name, Object input, ReferenceContext ref) {
return vcfToVariantContext(name, (VCFRecord)input, ref);
@ -168,7 +168,7 @@ public class VariantContextAdaptors {
Allele allele;
// special case: semi-deletion
if ( vcf.isDeletion() && refAllele.length() > alt.getLength() ) {
char[] semiDeletion = new char[refAllele.length() - alt.getLength()];
byte[] semiDeletion = new byte[refAllele.length() - alt.getLength()];
System.arraycopy(ref.getBases(), alt.getLength(), semiDeletion, 0, refAllele.length() - alt.getLength());
allele = new Allele(String.valueOf(semiDeletion), false);
} else {
@ -223,13 +223,16 @@ public class VariantContextAdaptors {
}
private static Allele determineRefAllele(VCFRecord vcf, ReferenceContext ref) {
if ( ref == null )
throw new StingException("Illegal determineRefAllele call!");
Allele refAllele;
if ( vcf.isInsertion() ) {
refAllele = new Allele(Allele.NULL_ALLELE_STRING, true);
} else if ( ref == null ) {
refAllele = new Allele(vcf.getReference(), true);
// } else if ( ref == null ) {
// refAllele = new Allele(vcf.getReference(), true);
} else if ( !vcf.isIndel() ) {
refAllele = new Allele(Character.toString(ref.getBase()), true);
refAllele = new Allele(ref.getBase(), true);
} else if ( vcf.isDeletion() ) {
int start = (int)(ref.getLocus().getStart() - ref.getWindow().getStart() + 1);
int delLength = 0;
@ -240,9 +243,7 @@ public class VariantContextAdaptors {
if ( delLength > ref.getWindow().getStop() - ref.getLocus().getStop() )
throw new IllegalArgumentException("Length of deletion is larger than reference context provided at " + ref.getLocus());
char[] deletion = new char[delLength];
System.arraycopy(ref.getBases(), start, deletion, 0, delLength);
refAllele = new Allele(String.valueOf(deletion), true);
refAllele = deletionAllele(ref, start, delLength);
} else {
throw new UnsupportedOperationException("Conversion of VCF type " + vcf.getType() + " is not supported.");
}
@ -250,6 +251,13 @@ public class VariantContextAdaptors {
return refAllele;
}
private static Allele deletionAllele(ReferenceContext ref, int start, int len) {
byte[] deletion = new byte[len];
System.arraycopy(ref.getBases(), start, deletion, 0, len);
return new Allele(deletion, true);
}
public static VCFHeader createVCFHeader(Set<VCFHeaderLine> hInfo, VariantContext vc) {
HashSet<String> names = new LinkedHashSet<String>();
for ( Genotype g : vc.getGenotypesSortedByName() ) {
@ -259,11 +267,11 @@ public class VariantContextAdaptors {
return new VCFHeader(hInfo == null ? new HashSet<VCFHeaderLine>() : hInfo, names);
}
public static VCFRecord toVCF(VariantContext vc, char vcfRefBase) {
public static VCFRecord toVCF(VariantContext vc, byte vcfRefBase) {
return toVCF(vc, vcfRefBase, null, true, false);
}
public static VCFRecord toVCF(VariantContext vc, char vcfRefBase, List<String> allowedGenotypeAttributeKeys, boolean filtersWereAppliedToContext, boolean filtersWereAppliedToGenotypes) {
public static VCFRecord toVCF(VariantContext vc, byte vcfRefBase, List<String> allowedGenotypeAttributeKeys, boolean filtersWereAppliedToContext, boolean filtersWereAppliedToGenotypes) {
// deal with the reference
String referenceBases = new String(vc.getReference().getBases());
@ -293,21 +301,21 @@ public class VariantContextAdaptors {
if ( a.isNull() ) {
if ( a.isReference() ) {
// ref, where alt is insertion
encoding = new VCFGenotypeEncoding(Character.toString(vcfRefBase));
encoding = new VCFGenotypeEncoding(Character.toString((char)vcfRefBase));
} else {
// non-ref deletion
encoding = new VCFGenotypeEncoding("D" + Integer.toString(referenceBases.length()));
}
} else if ( a.isReference() ) {
// ref, where alt is deletion
encoding = new VCFGenotypeEncoding(Character.toString(vcfRefBase));
encoding = new VCFGenotypeEncoding(Character.toString((char)vcfRefBase));
} else {
// non-ref insertion
encoding = new VCFGenotypeEncoding("I" + alleleString);
}
} else if ( vc.getType() == VariantContext.Type.NO_VARIATION ) {
// ref
encoding = new VCFGenotypeEncoding(Character.toString(vcfRefBase));
encoding = new VCFGenotypeEncoding(Character.toString((char)vcfRefBase));
} else {
// ref or alt for snp
encoding = new VCFGenotypeEncoding(alleleString);
@ -381,7 +389,7 @@ public class VariantContextAdaptors {
infoFields.put(key, outputValue);
}
return new VCFRecord(Character.toString(vcfRefBase), contig, position, ID, vcfAltAlleles, qual, filters, infoFields, genotypeFormatString, genotypeObjects);
return new VCFRecord(Character.toString((char)vcfRefBase), contig, position, ID, vcfAltAlleles, qual, filters, infoFields, genotypeFormatString, genotypeObjects);
}
private static String formatVCFField(String key, Object val) {
@ -389,7 +397,7 @@ public class VariantContextAdaptors {
if ( val == null )
result = VCFGenotypeRecord.getMissingFieldValue(key);
else if ( val instanceof Double )
result = String.format("%.2f", val);
result = String.format("%.2f", (Double)val);
else
result = val.toString();
@ -418,9 +426,9 @@ public class VariantContextAdaptors {
// --------------------------------------------------------------------------------------------------------------
private static class PlinkRodAdaptor extends VCAdaptor {
VariantContext convert(String name, Object input) {
return convert(name, input, null);
}
// VariantContext convert(String name, Object input) {
// return convert(name, input, null);
// }
VariantContext convert(String name, Object input, ReferenceContext ref) {
if ( ref == null )
@ -487,16 +495,15 @@ public class VariantContextAdaptors {
private Allele determineRefAllele(PlinkRod plink, ReferenceContext ref) {
Allele refAllele;
if ( !plink.isIndel() ) {
refAllele = new Allele(Character.toString(ref.getBase()), true);
refAllele = new Allele(ref.getBase(), true);
} else if ( plink.isInsertion() ) {
refAllele = new Allele(Allele.NULL_ALLELE_STRING, true);
} else {
long maxLength = ref.getWindow().getStop() - ref.getLocus().getStop();
if ( plink.getLength() > maxLength )
throw new UnsupportedOperationException("Plink conversion currently can only handle indels up to length " + maxLength);
char[] deletion = new char[plink.getLength()];
System.arraycopy(ref.getBases(), 1, deletion, 0, plink.getLength());
refAllele = new Allele(String.valueOf(deletion), true);
refAllele = deletionAllele(ref, 1, plink.getLength());
}
return refAllele;
}
@ -588,9 +595,9 @@ public class VariantContextAdaptors {
* @param input the Rod object, in this case a RodGeliText
* @return a VariantContext object
*/
VariantContext convert(String name, Object input) {
return convert(name, input, null);
}
// VariantContext convert(String name, Object input) {
// return convert(name, input, null);
// }
/**
* convert to a Variant Context, given:
@ -656,9 +663,9 @@ public class VariantContextAdaptors {
* @param input the Rod object, in this case a RodGeliText
* @return a VariantContext object
*/
VariantContext convert(String name, Object input) {
return convert(name, input, null);
}
// VariantContext convert(String name, Object input) {
// return convert(name, input, null);
// }
/**
* convert to a Variant Context, given:
@ -729,9 +736,9 @@ public class VariantContextAdaptors {
* @param input the Rod object, in this case a RodGeliText
* @return a VariantContext object
*/
VariantContext convert(String name, Object input) {
return convert(name, input, null);
}
// VariantContext convert(String name, Object input) {
// return convert(name, input, null);
// }
/**
* convert to a Variant Context, given:
@ -748,7 +755,7 @@ public class VariantContextAdaptors {
// add the reference allele
HashSet<Allele> alleles = new HashSet<Allele>();
Allele refAllele = new Allele(Character.toString(ref.getBase()), true);
Allele refAllele = new Allele(ref.getBase(), true);
alleles.add(refAllele);
// make a mapping from sample to genotype

12
java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
View File

@ -3,11 +3,13 @@ package org.broadinstitute.sting.gatk.traversals;
import net.sf.samtools.SAMRecord;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.WalkerManager;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.providers.*;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLoc;
/*
* Copyright (c) 2009 The Broad Institute
@ -77,12 +79,12 @@ public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,Read
// while we still have more reads
for (SAMRecord read : reads) {
// an array of characters that represent the reference
char[] refSeq = null;
// ReferenceContext -- the reference bases covered by the read
ReferenceContext refContext = null;
// get the array of characters for the reference sequence, since we're a mapped read
if (needsReferenceBasesP && !read.getReadUnmappedFlag() && dataProvider.hasReference())
refSeq = reference.getReferenceBases(read);
refContext = reference.getReferenceContext(read);
// update the number of reads we've seen
TraversalStatistics.nRecords++;
@ -91,9 +93,9 @@ public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,Read
// if the read is mapped, create a metadata tracker
ReadMetaDataTracker tracker = (read.getReferenceIndex() >= 0) ? rodView.getReferenceOrderedDataForRead(read) : null;
final boolean keepMeP = walker.filter(refSeq, read);
final boolean keepMeP = walker.filter(refContext, read);
if (keepMeP) {
M x = walker.map(refSeq, read, tracker); // the tracker can be null
M x = walker.map(refContext, read, tracker); // the tracker can be null
sum = walker.reduce(x, sum);
}

3
java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
View File

@ -34,6 +34,7 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import java.util.*;
import java.util.regex.Pattern;
@ -168,7 +169,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
* @param read the read itself, as a SAMRecord
* @return the ReadClipper object describing what should be done to clip this read
*/
public ReadClipper map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public ReadClipper map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
ReadClipper clipper = new ReadClipper(read);

3
java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java
View File

@ -38,6 +38,7 @@ package org.broadinstitute.sting.gatk.walkers;
*/
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.commandline.Argument;
import net.sf.samtools.SAMFileWriter;
@ -62,7 +63,7 @@ public class FixBAMSortOrderTag extends ReadWalker<SAMRecord, SAMFileWriter> {
public SAMFileHeader.SortOrder SORT_ORDER=SAMFileHeader.SortOrder.coordinate;
@Override
public SAMRecord map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public SAMRecord map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
return read;
}

3
java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
View File

@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import java.text.DecimalFormat;
import java.text.NumberFormat;
@ -113,7 +114,7 @@ public class FlagStatWalker extends ReadWalker<Integer, Integer> {
private FlagStat myStat = new FlagStat();
public Integer map( char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
public Integer map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
myStat.readCount++;
if (read.getReadFailsVendorQualityCheckFlag()) {
myStat.QC_failure++;

2
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
View File

@ -89,7 +89,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
if(shouldShowSecondaryBasePileup(basePileup))
secondBasePileup = getSecondBasePileup(basePileup);
out.printf("%s%s %s%n", basePileup.getPileupString(ref.getBase()), secondBasePileup, rods);
out.printf("%s%s %s%n", basePileup.getPileupString(ref.getBaseAsChar()), secondBasePileup, rods);
}
if ( context.hasExtendedEventPileup() ) {

5
java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
View File

@ -29,6 +29,7 @@ import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
/**
@ -63,7 +64,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
* @param read the read itself, as a SAMRecord
* @return true if the read passes the filter, false if it doesn't
*/
public boolean filter(char[] ref, SAMRecord read) {
public boolean filter(ReferenceContext ref, SAMRecord read) {
// check the read group
if ( readGroup != null ) {
SAMReadGroupRecord myReadGroup = read.getReadGroup();
@ -91,7 +92,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
* @param read the read itself, as a SAMRecord
* @return the read itself
*/
public SAMRecord map( char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
return read;
}

5
java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
View File

@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
/**
* Created by IntelliJ IDEA.
@ -18,11 +19,11 @@ public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, Re
/** Must return true for reads that need to be processed. Reads, for which this method return false will
* be skipped by the engine and never passed to the walker.
*/
public boolean filter(char[] ref, SAMRecord read) {
public boolean filter(ReferenceContext ref, SAMRecord read) {
// We are keeping all the reads
return true;
}
// Map over the org.broadinstitute.sting.gatk.contexts.AlignmentContext
public abstract MapType map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker);
public abstract MapType map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker);
}

3
java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.apache.log4j.Logger;
@ -53,7 +54,7 @@ public class SplitSamFileWalker extends ReadWalker<SAMRecord, Map<String, SAMFil
logger.info("SplitSamFile version: " + VERSION);
}
public SAMRecord map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public SAMRecord map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
return read;
}

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

@ -30,7 +30,7 @@ public class GCContent implements InfoFieldAnnotation, ExperimentalAnnotation {
private static double computeGCContent(ReferenceContext ref) {
int gc = 0, at = 0;
for ( char base : ref.getBases() ) {
for ( byte base : ref.getBases() ) {
int baseIndex = BaseUtils.simpleBaseToBaseIndex(base);
if ( baseIndex == BaseUtils.gIndex || baseIndex == BaseUtils.cIndex )
gc++;

12
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
View File

@ -24,7 +24,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
int run;
if ( vc.isSNP() ) {
run = computeHomopolymerRun(vc.getAlternateAllele(0).toString().charAt(0), ref);
run = computeHomopolymerRun(vc.getAlternateAllele(0).getBases()[0], ref);
} else if ( vc.isIndel() && ANNOTATE_INDELS ) {
run = computeIndelHomopolymerRun(vc,ref);
} else {
@ -42,12 +42,12 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
public boolean useZeroQualityReads() { return false; }
private static int computeHomopolymerRun(char altAllele, ReferenceContext ref) {
private static int computeHomopolymerRun(byte altAllele, ReferenceContext ref) {
// TODO -- this needs to be computed in a more accurate manner
// We currently look only at direct runs of the alternate allele adjacent to this position
char[] bases = ref.getBases();
byte[] bases = ref.getBases();
GenomeLoc window = ref.getWindow();
GenomeLoc locus = ref.getLocus();
@ -71,13 +71,13 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
}
private static int computeIndelHomopolymerRun(VariantContext vc, ReferenceContext ref) {
char[] bases = ref.getBases();
byte[] bases = ref.getBases();
GenomeLoc locus = ref.getLocus();
GenomeLoc window = ref.getWindow();
int refBasePos = (int) (locus.getStart() - window.getStart())+1;
if ( vc.isDeletion() ) {
// check that deleted bases are the same
char dBase = bases[refBasePos];
byte dBase = bases[refBasePos];
for ( int i = 0; i < vc.getAlternateAllele(0).length(); i ++ ) {
if ( bases[refBasePos+i] != dBase ) {
return 0;
@ -87,7 +87,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
return computeHomopolymerRun(dBase,ref);
} else {
// check that inserted bases are the same
char insBase = (char) vc.getAlternateAllele(0).getBases()[0];
byte insBase = vc.getAlternateAllele(0).getBases()[0];
for ( byte b : vc.getAlternateAllele(0).getBases() ) {
if ( insBase != (char) b ) {
return 0;

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

@ -37,7 +37,7 @@ public abstract class RankSumTest implements InfoFieldAnnotation, WorkInProgress
if ( context == null )
continue;
fillQualsFromPileup(ref.getBase(), vc.getAlternateAllele(0).toString().charAt(0), context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), refQuals, altQuals);
fillQualsFromPileup(ref.getBaseAsChar(), vc.getAlternateAllele(0).toString().charAt(0), context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), refQuals, altQuals);
}
}

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

@ -68,7 +68,7 @@ public class SecondBaseSkew implements InfoFieldAnnotation, ExperimentalAnnotati
Pair<Integer, Integer> depth = new Pair<Integer, Integer>(0, 0);
for ( String sample : stratifiedContexts.keySet() ) {
//Pair<Integer,Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBase(),stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getPileup(), alternate);
Pair<Integer, Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBase(), stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), alternate);
Pair<Integer, Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBaseAsChar(), stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), alternate);
depth.first += sampleDepth.first;
depth.second += sampleDepth.second;
}

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

@ -171,7 +171,7 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
return 0;
Object variant = rods.get(0);
VariantContext vc = VariantContextAdaptors.toVariantContext("variant", variant);
VariantContext vc = VariantContextAdaptors.toVariantContext("variant", variant, ref);
if ( vc == null )
return 0;

6
java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java
View File

@ -77,12 +77,12 @@ public class IndelSubsets implements ConcordanceType {
}
private int homopolymerRunSize(ReferenceContext ref, VCFRecord indel) {
char[] bases = ref.getBases();
byte[] bases = ref.getBases();
GenomeLoc window = ref.getWindow();
GenomeLoc locus = ref.getLocus();
int refBasePos = (int)(locus.getStart() - window.getStart());
char indelBase = indel.isDeletion() ? bases[refBasePos+1] : indel.getAlternateAlleleList().get(0).charAt(0);
byte indelBase = indel.isDeletion() ? bases[refBasePos+1] : (byte)indel.getAlternateAlleleList().get(0).charAt(0);
int leftRun = 0;
for ( int i = refBasePos; i >= 0; i--) {
if ( bases[i] != indelBase )
@ -90,7 +90,7 @@ public class IndelSubsets implements ConcordanceType {
leftRun++;
}
indelBase = indel.isDeletion() ? bases[Math.min(refBasePos+indel.getAlternateAlleleList().get(0).length(),bases.length-1)] : indel.getAlternateAlleleList().get(0).charAt(indel.getAlternateAlleleList().get(0).length()-1);
indelBase = indel.isDeletion() ? bases[Math.min(refBasePos+indel.getAlternateAlleleList().get(0).length(),bases.length-1)] : (byte)indel.getAlternateAlleleList().get(0).charAt(indel.getAlternateAlleleList().get(0).length()-1);
int rightRun = 0;
for ( int i = refBasePos + (indel.isDeletion() ? 1+indel.getAlternateAlleleList().get(0).length() : 1); i < bases.length; i++) {
if ( bases[i] != indelBase )

4
java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java
View File

@ -31,7 +31,7 @@ public class SNPGenotypeConcordance implements ConcordanceType {
}
public String computeConcordance(Map<String, VCFGenotypeRecord> samplesToRecords, ReferenceContext ref) {
char refBase = ref.getBase();
char refBase = ref.getBaseAsChar();
VCFGenotypeRecord call1 = samplesToRecords.get(sample1);
if ( call1 != null && call1.isNoCall() )
@ -90,7 +90,7 @@ public class SNPGenotypeConcordance implements ConcordanceType {
// are they the same genotype
if ( genotype1.equals(genotype2) )
result.append("sameGenotype");
else if ( sameVariantAllele(genotype1, genotype2, ref.getBase()) )
else if ( sameVariantAllele(genotype1, genotype2, ref.getBaseAsChar()) )
result.append("differentGenotypeSameVariantAllele");
else
result.append("differentVariantAllele");

3
java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
View File

@ -29,6 +29,7 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
/**
@ -54,7 +55,7 @@ public class CoarseCoverageWalker extends ReadWalker<Integer,Integer> {
}
@Override
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
if ( read.getReadUnmappedFlag() ||
read.getDuplicateReadFlag() ||

3
java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java
View File

@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.fasta;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.commandline.Argument;
import net.sf.samtools.SAMRecord;
@ -59,7 +60,7 @@ public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
}
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
out.println("@" + read.getReadName());
if ( !RE_REVERSE || !read.getReadNegativeStrandFlag() ) {
out.println(read.getReadString());

2
java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
View File

@ -53,7 +53,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
return new Pair<GenomeLoc, String>(context.getLocation(), "");
}
String refBase = String.valueOf(ref.getBase());
String refBase = String.valueOf(ref.getBaseAsChar());
for ( VariantContext vc : tracker.getAllVariantContexts(ref) ) {
// if we have multiple variants at a locus, just take the first one we see

2
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
View File

@ -142,7 +142,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
if ( rods.size() == 0 )
return 0;
VariantContext vc = VariantContextAdaptors.toVariantContext("variant", rods.get(0));
VariantContext vc = VariantContextAdaptors.toVariantContext("variant", rods.get(0), ref);
FiltrationContext varContext = new FiltrationContext(tracker, ref, vc);
// if we're still initializing the context, do so

4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
View File

@ -9,6 +9,8 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
import java.util.*;
import net.sf.samtools.util.SequenceUtil;
public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
private int MIN_COVERAGE = 6;
@ -100,7 +102,7 @@ public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
// calculate the sum of quality scores for each base
ReadBackedExtendedEventPileup pileup = context.getExtendedEventPileup();
List<Pair<String,Integer>> all_events = pileup.getEventStringsWithCounts(ref);
List<Pair<String,Integer>> all_events = pileup.getEventStringsWithCounts(BaseUtils.charSeq2byteSeq(ref));
for ( Pair<String,Integer> p : all_events ) {
if ( p.second > bestIndelCount ) {
bestIndelCount = p.second;

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -159,7 +159,7 @@ public class UnifiedGenotyperEngine {
gcm.set(GenotypeCalculationModelFactory.makeGenotypeCalculation(samples, logger, UAC, format, verboseWriter, beagleWriter));
}
char ref = Character.toUpperCase(refContext.getBase());
char ref = Character.toUpperCase(refContext.getBaseAsChar());
if ( !BaseUtils.isRegularBase(ref) )
return null;

9
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
View File

@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODItera
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.collections.CircularArray;
@ -178,7 +179,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
@Override
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
// if ( read.getReadName().equals("428EFAAXX090610:2:36:1384:639#0") ) System.out.println("GOT READ");
@ -294,9 +295,9 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
if ( rg == null ) throw new StingException("Read "+read.getReadName()+" has no read group in merged stream. RG is required for somatic calls.");
if ( normalReadGroups.contains(rg) ) {
normal_context.add(read,ref);
normal_context.add(read,ref.getBasesAsChars());
} else if ( tumorReadGroups.contains(rg) ) {
tumor_context.add(read,ref);
tumor_context.add(read,ref.getBasesAsChars());
} else {
throw new StingException("Unrecognized read group in merged stream: "+rg);
}
@ -315,7 +316,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
} else {
normal_context.add(read, ref);
normal_context.add(read, ref.getBasesAsChars());
if ( normal_context.getReads().size() > MAX_READ_NUMBER ) {
System.out.println("WARNING: a count of "+MAX_READ_NUMBER+" reads reached in a window "+
refName+':'+normal_context.getStart()+'-'+normal_context.getStop()+". The whole window will be dropped");

13
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -30,6 +30,7 @@ import net.sf.samtools.util.StringUtil;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
@ -283,7 +284,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
if ( currentInterval == null ) {
emit(read);
return 0;
@ -314,9 +315,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ) {
readsNotToClean.add(read);
} else {
readsToClean.add(read, ref);
readsToClean.add(read, ref.getBasesAsChars());
// add the rods to the list of known variants
populateKnownIndels(metaDataTracker);
populateKnownIndels(metaDataTracker, null); // todo -- fixme!
}
if ( readsToClean.size() + readsNotToClean.size() >= MAX_READS ) {
@ -335,7 +336,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
return 0;
}
private void cleanAndCallMap(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
private void cleanAndCallMap(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
clean(readsToClean);
knownIndelsToTry.clear();
@ -403,7 +404,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
}
private void populateKnownIndels(ReadMetaDataTracker metaDataTracker) {
private void populateKnownIndels(ReadMetaDataTracker metaDataTracker, ReferenceContext ref) {
for ( Collection<GATKFeature> rods : metaDataTracker.getContigOffsetMapping().values() ) {
Iterator<GATKFeature> rodIter = rods.iterator();
while ( rodIter.hasNext() ) {
@ -411,7 +412,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( knownIndelsToTry.containsKey(rod) )
continue;
if ( VariantContextAdaptors.canBeConvertedToVariantContext(rod))
knownIndelsToTry.put(rod, VariantContextAdaptors.toVariantContext("", rod));
knownIndelsToTry.put(rod, VariantContextAdaptors.toVariantContext("", rod, ref));
else
knownIndelsToTry.put(rod, null);
}

2
java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
View File

@ -123,7 +123,7 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
if ( pileup != null ) {
int mismatchQualities = 0, totalQualities = 0;
char upperRef = Character.toUpperCase(ref.getBase());
char upperRef = Character.toUpperCase(ref.getBaseAsChar());
for (PileupElement p : pileup ) {
// check the ends of the reads to see how far they extend
SAMRecord read = p.getRead();

3
java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
View File

@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
/**
* Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
@ -13,7 +14,7 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
*/
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountReadsWalker extends ReadWalker<Integer, Integer> {
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker tracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
//System.out.println(read.format());
return 1;
}

3
java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
View File

@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.commandline.Argument;
@ -104,7 +105,7 @@ public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
if ( AlignmentUtils.isReadUnmapped(read) && MAPPED_ONLY) return 0;

2
java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
View File

@ -16,7 +16,7 @@ import net.sf.samtools.SAMRecord;
*/
public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integer> implements TreeReducible<Integer> {
public AlignmentContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
out.printf( "In map: ref = %s, loc = %s, reads = %s%n", ref.getBase(),
out.printf( "In map: ref = %s, loc = %s, reads = %s%n", ref.getBaseAsChar(),
context.getLocation(),
Arrays.deepToString( getReadNames(context.getReads()) ) );
return context;

3
java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java
View File

@ -26,6 +26,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.MathUtils;
@ -67,7 +68,7 @@ public class ReadClippingStatsWalker extends ReadWalker<ReadClippingStatsWalker.
int readLength, nClippingEvents, nClippedBases;
}
public ReadClippingInfo map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public ReadClippingInfo map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
if ( AlignmentUtils.isReadUnmapped(read) && MAPPED_ONLY)
return null;

5
java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
View File

@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.StingException;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileWriter;
@ -67,7 +68,7 @@ public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
* @param read the read itself, as a SAMRecord
* @return true if the read passes the filter, false if it doesn't
*/
public boolean filter(char[] ref, SAMRecord read) {
public boolean filter(ReferenceContext ref, SAMRecord read) {
return true;
}
@ -77,7 +78,7 @@ public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
* @param read the read itself, as a SAMRecord
* @return the read itself
*/
public SAMRecord map( char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
return read;
}

4
java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
View File

@ -54,7 +54,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
SAMPileupFeature truePileup = getTruePileup( tracker );
if ( truePileup == null ) {
out.printf("No truth pileup data available at %s%n", pileup.getPileupString(ref.getBase()));
out.printf("No truth pileup data available at %s%n", pileup.getPileupString(ref.getBaseAsChar()));
if ( ! CONTINUE_AFTER_AN_ERROR ) {
Utils.scareUser(String.format("No pileup data available at %s given GATK's output of %s -- this walker requires samtools pileup data over all bases",
context.getLocation(), new String(pileup.getBases())));
@ -62,7 +62,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
} else {
String pileupDiff = pileupDiff(pileup, truePileup, true);
if ( pileupDiff != null ) {
out.printf("%s vs. %s%n", pileup.getPileupString(ref.getBase()), truePileup.getPileupString());
out.printf("%s vs. %s%n", pileup.getPileupString(ref.getBaseAsChar()), truePileup.getPileupString());
if ( ! CONTINUE_AFTER_AN_ERROR ) {
throw new RuntimeException(String.format("Pileups aren't equal: %s", pileupDiff));
}

6
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
View File

@ -298,7 +298,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
if( gatkRead.getBaseQualities()[offset] > 0 ) {
bases = gatkRead.getReadBases();
refBase = (byte)ref.getBase();
refBase = ref.getBase();
// Skip if this base is an 'N' or etc.
if( BaseUtils.isRegularBase( (char)(bases[offset]) ) ) {
@ -345,9 +345,9 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
* @param context The AlignmentContext which holds the reads covered by this locus
* @param ref The reference base
*/
private static void updateMismatchCounts(final Pair<Long, Long> counts, final AlignmentContext context, final char ref) {
private static void updateMismatchCounts(final Pair<Long, Long> counts, final AlignmentContext context, final byte ref) {
for( PileupElement p : context.getBasePileup() ) {
final char readChar = (char)(p.getBase());
final byte readChar = p.getBase();
final int readCharBaseIndex = BaseUtils.simpleBaseToBaseIndex(readChar);
final int refCharBaseIndex = BaseUtils.simpleBaseToBaseIndex(ref);

9
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
View File

@ -49,6 +49,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.classloader.PackageUtils;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
@ -316,7 +317,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
* @param read The read to be recalibrated
* @return The read with quality scores replaced
*/
public SAMRecord map( char[] refBases, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
public SAMRecord map( ReferenceContext refBases, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
RecalDataManager.parseSAMRecord( read, RAC );
@ -332,7 +333,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
return read; // can't recalibrate a SOLiD read with no calls in the color space, and the user wants to skip over them
}
}
originalQuals = RecalDataManager.calcColorSpace( read, originalQuals, RAC.SOLID_RECAL_MODE, coinFlip, refBases );
originalQuals = RecalDataManager.calcColorSpace( read, originalQuals, RAC.SOLID_RECAL_MODE, coinFlip, refBases == null ? null : refBases.getBasesAsChars() );
}
//compute all covariate values for this read
@ -360,9 +361,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
if ( read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG) == null ) { // Save the old qualities if the tag isn't already taken in the read
read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, QualityUtils.phredToFastq(originalQuals));
}
if (read.getAttribute(SAMTag.UQ.name()) != null) {
// TODO - When refBases is switches to byte[], call the appropriate overload in SAM-JDK, and remove char[] overload from SAM-JDK.
read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, refBases, read.getAlignmentStart() - 1));
read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, refBases.getBases(), read.getAlignmentStart() - 1, false));
}
return read;

10
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
View File

@ -92,8 +92,6 @@ public class PickSequenomProbes extends RodWalker<String, String> {
logger.debug("Probing " + ref.getLocus() + " " + ref.getWindow());
String refBase = String.valueOf(ref.getBase());
Collection<VariantContext> VCs = tracker.getAllVariantContexts(ref);
if ( VCs.size() == 0 )
return "";
@ -128,7 +126,7 @@ public class PickSequenomProbes extends RodWalker<String, String> {
}
}
char[] context_bases = ref.getBases();
byte[] context_bases = ref.getBases();
for (int i = 0; i < 401; i++) {
if ( maskFlags[i] == 1 ) {
context_bases[i] = 'N';
@ -140,11 +138,11 @@ public class PickSequenomProbes extends RodWalker<String, String> {
String assay_sequence;
if ( vc.isSNP() )
assay_sequence = leading_bases + "[" + refBase + "/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
assay_sequence = leading_bases + "[" + ref.getBaseAsChar() + "/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
else if ( vc.isInsertion() )
assay_sequence = leading_bases + refBase + "[-/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
assay_sequence = leading_bases + ref.getBaseAsChar() + "[-/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
else if ( vc.isDeletion() )
assay_sequence = leading_bases + refBase + "[" + new String(vc.getReference().getBases()) + "/-]" + trailing_bases.substring(vc.getReference().length());
assay_sequence = leading_bases + ref.getBaseAsChar() + "[" + new String(vc.getReference().getBases()) + "/-]" + trailing_bases.substring(vc.getReference().length());
else
return "";

14
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -441,7 +441,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
//System.out.printf("map at %s with %d skipped%n", context.getLocation(), context.getSkippedBases());
Map<String, VariantContext> vcs = getVariantContexts(tracker, context);
Map<String, VariantContext> vcs = getVariantContexts(ref, tracker, context);
//Collection<VariantContext> comps = getCompVariantContexts(tracker, context);
// to enable walking over pairs where eval or comps have no elements
@ -493,7 +493,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
return 0;
}
private void writeInterestingSite(List<String> interestingReasons, VariantContext vc, char ref) {
private void writeInterestingSite(List<String> interestingReasons, VariantContext vc, byte ref) {
if ( vc != null && writer != null && interestingReasons.size() > 0 ) {
// todo -- the vc == null check is because you can be interesting because you are a FN, and so VC == null
MutableVariantContext mvc = new MutableVariantContext(vc);
@ -576,21 +576,21 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
//
//logger.info(String.format("Ignore second+ events at locus %s in rod %s => rec is %s", context.getLocation(), rodList.getName(), rec));
private Map<String, VariantContext> getVariantContexts(RefMetaDataTracker tracker, AlignmentContext context) {
private Map<String, VariantContext> getVariantContexts(ReferenceContext ref, RefMetaDataTracker tracker, AlignmentContext context) {
// todo -- we need to deal with dbSNP where there can be multiple records at the same start site. A potential solution is to
// todo -- allow the variant evaluation to specify the type of variants it wants to see and only take the first such record at a site
Map<String, VariantContext> bindings = new HashMap<String, VariantContext>();
if ( tracker != null ) {
bindVariantContexts(bindings, evalNames, tracker, context, false);
bindVariantContexts(bindings, compNames, tracker, context, true);
bindVariantContexts(ref, bindings, evalNames, tracker, context, false);
bindVariantContexts(ref, bindings, compNames, tracker, context, true);
}
return bindings;
}
private void bindVariantContexts(Map<String, VariantContext> map, Collection<String> names,
private void bindVariantContexts(ReferenceContext ref, Map<String, VariantContext> map, Collection<String> names,
RefMetaDataTracker tracker, AlignmentContext context, boolean allowExcludes ) {
for ( String name : names ) {
Collection<VariantContext> contexts = tracker.getVariantContexts(name, ALLOW_VARIANT_CONTEXT_TYPES, context.getLocation(), true, true);
Collection<VariantContext> contexts = tracker.getVariantContexts(ref, name, ALLOW_VARIANT_CONTEXT_TYPES, context.getLocation(), true, true);
if ( contexts.size() > 1 )
throw new StingException("Found multiple variant contexts at " + context.getLocation());

2
java/src/org/broadinstitute/sting/gatk/walkers/vcf/FilterLiftedVCF.java
View File

@ -80,7 +80,7 @@ public class FilterLiftedVCF extends RodWalker<Integer, Integer> {
List<Object> rods = tracker.getReferenceMetaData("vcf");
for ( Object rod : rods )
filterAndWrite(ref.getBase(), (VCFRecord)rod);
filterAndWrite(ref.getBaseAsChar(), (VCFRecord)rod);
return 0;
}

8
java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java
View File

@ -350,14 +350,14 @@ public class MultiSampleCaller extends LocusWalker<MultiSampleCaller.MultiSample
context = filter_each_read(context);
if (ref.getBase() == 'N') { return null; }
if (ref.getBaseAsChar() == 'N') { return null; }
if (BaseUtils.simpleBaseToBaseIndex(ref.getBase()) == -1) { return null; }
if (context.getReads().size() <= 0) { return null; }
if (context.getReads().size() >= 10000) { return null; } // to deal with big piles -- totally arbitrary threshold
this.ref = ref.getBase();
MultiSampleCallResult result = this.MultiSampleCall(tracker, ref.getBase(), context, sample_names);
if ( INCLUDE_STATS ) stats_output_file.println(DepthStats.Row(ref.getBase(), context));
this.ref = ref.getBaseAsChar();
MultiSampleCallResult result = this.MultiSampleCall(tracker, ref.getBaseAsChar(), context, sample_names);
if ( INCLUDE_STATS ) stats_output_file.println(DepthStats.Row(ref.getBaseAsChar(), context));
return result;
}

3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlignedReadsHistoWalker.java
View File

@ -4,6 +4,7 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
/**
* Created by IntelliJ IDEA.
@ -28,7 +29,7 @@ public class AlignedReadsHistoWalker extends ReadWalker<Integer, Integer> {
return !read.getReadUnmappedFlag();
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
//System.out.println(read.getAttribute("NM"));
int editDist = Integer.parseInt(read.getAttribute("NM").toString());
if (editDist <= 50)

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java
View File

@ -104,7 +104,7 @@ public class AlleleBalanceHistogramWalker extends LocusWalker<Map<String,Double>
}
for ( PileupElement e : alicon.getBasePileup() ) {
if ( BaseUtils.basesAreEqual( e.getBase(), (byte) ref.getBase() ) ) {
if ( BaseUtils.basesAreEqual( e.getBase(), ref.getBase() ) ) {
refBases++;
} else if ( BaseUtils.basesAreEqual(e.getBase(), (byte) snpBase ) ) {
altBases++;

10
java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java
View File

@ -230,7 +230,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
public void updateTable(BaseTransitionTable t, SAMRecord r, int o, ReferenceContext ref) {
// System.out.println("Update Table");
if ( r.getReadNegativeStrandFlag() ) {
t.update(BaseUtils.simpleComplement((char) r.getReadBases()[o]),BaseUtils.simpleComplement(ref.getBase()));
t.update((byte)BaseUtils.simpleComplement((char) r.getReadBases()[o]), (byte)BaseUtils.simpleComplement(ref.getBaseAsChar()));
} else {
t.update(r.getReadBases()[o], ref.getBase());
}
@ -353,7 +353,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
return String.format("%s\t%s%n",header,"Counts");
}
public int countMismatches(char ref, ReadBackedPileup p) {
public int countMismatches(byte ref, ReadBackedPileup p) {
int refM = p.getBaseCounts()[BaseUtils.simpleBaseToBaseIndex(ref)];
return p.size()-refM;
}
@ -477,7 +477,7 @@ class BaseTransitionTable implements Comparable {
out.print(s.toString());
}
public void update(char observedBase, char refBase ) {
public void update(byte observedBase, byte refBase ) {
//if ( observedBase == refBase ) {
// throw new StingException("BaseTransitionTable received equal observed and reference bases, which should not happen.");
//}
@ -485,10 +485,6 @@ class BaseTransitionTable implements Comparable {
table[BaseUtils.simpleBaseToBaseIndex(observedBase)][BaseUtils.simpleBaseToBaseIndex(refBase)]++;
}
public void update(byte observed, char ref) {
update( (char) observed, ref);
}
public int numConditions() {
return conditions.size();
}

3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/DSBWalkerV3.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
@ -353,7 +354,7 @@ public class DSBWalkerV3 extends ReadWalker<Integer,Integer> {
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
if ( AlignmentUtils.isReadUnmapped(read) ) return 0;

3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/IOCrusherWalker.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import net.sf.samtools.SAMRecord;
@ -63,7 +64,7 @@ public class IOCrusherWalker extends ReadWalker<SAMRecord, ArrayList<SAMFileWrit
/**
*
*/
public SAMRecord map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public SAMRecord map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
nReadsRead++;
return read;
}

6
java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
View File

@ -95,7 +95,7 @@ public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator>
tracker.getReferenceMetaData("comp").size() != 0 ? tracker.getReferenceMetaData("comp").get(0) : null;
VariantContext compContext;
if ( comp != null ) {
compContext = VariantContextAdaptors.toVariantContext("comp",comp);
compContext = VariantContextAdaptors.toVariantContext("comp",comp, ref);
} else {
compContext = null;
}
@ -142,12 +142,12 @@ public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator>
if ( vcfWriter != null ) {
int i = 0;
while ( i < compContexts.size() && compContexts.get(i).getLocation().isBefore(evalContexts.get(0).getLocation())) {
vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),(char)compContexts.get(i).getReference().getBases()[0]));
vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),compContexts.get(i).getReference().getBases()[0]));
i++;
}
vcfWriter.addRecord(VariantContextAdaptors.toVCF(evalContexts.get(0),ref.getBase()));
while ( i < compContexts.size() && compContexts.get(i).getLocation().distance(evalContexts.get(0).getLocation()) <= indelWindow) {
vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),(char) compContexts.get(i).getReference().getBases()[0]));
vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),compContexts.get(i).getReference().getBases()[0]));
i++;
}
}

7
java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchCounterWalker.java
View File

@ -4,24 +4,25 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.Utils;
import java.util.List;
@WalkerName("CountMismatches")
public class MismatchCounterWalker extends ReadWalker<Integer, Integer> {
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
int nMismatches = 0;
int start = read.getAlignmentStart()-1;
int stop = read.getAlignmentEnd();
// sometimes BWA outputs screwy reads
if ( stop - start > ref.length )
if ( stop - start > ref.getBases().length )
return 0;
if ( read.getAlignmentBlocks().size() == 1 ) {
// No indels
List<Byte> refSeq = Utils.subseq(ref);
List<Byte> refSeq = Utils.subseq(ref.getBases());
List<Byte> readBases = Utils.subseq(read.getReadBases());
assert(refSeq.size() == readBases.size());

11
java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchHistoWalker.java
View File

@ -4,6 +4,7 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.Utils;
import java.util.List;
@ -17,12 +18,12 @@ public class MismatchHistoWalker extends ReadWalker<Integer, Integer> {
protected final int MAX_TARGET_EDIT_DISTANCE = 10;
// Do we actually want to operate on the context?
public boolean filter(char[] ref, SAMRecord read) {
public boolean filter(ReferenceContext ref, SAMRecord read) {
// we only want aligned reads
return !read.getReadUnmappedFlag();
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
int editDist = Integer.parseInt(read.getAttribute("NM").toString());
@ -34,15 +35,15 @@ public class MismatchHistoWalker extends ReadWalker<Integer, Integer> {
int start = read.getAlignmentStart()-1;
int stop = read.getAlignmentEnd();
// sometimes BWA outputs screwy reads
if ( stop - start > ref.length )
if ( stop - start > ref.getBases().length )
return 0;
List<Byte> refSeq = Utils.subseq(ref);
List<Byte> refSeq = Utils.subseq(ref.getBases());
List<Byte> readBases = Utils.subseq(read.getReadBases());
assert(refSeq.size() == readBases.size());
// it's actually faster to reallocate a resized array than to use ArrayLists...
if ( ref.length > mismatchCounts.length ) {
if ( ref.getBases().length > mismatchCounts.length ) {
int oldLength = mismatchCounts.length;
mismatchCounts = (long[])resizeArray(mismatchCounts, refSeq.size());
for ( int i = oldLength; i < refSeq.size(); i++ )

3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/PairedQualityScoreCountsWalker.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.BaseUtils;
@ -61,7 +62,7 @@ public class PairedQualityScoreCountsWalker extends ReadWalker<Pair<byte[],Boole
return reduceCounts;
}
public Pair<byte[],Boolean> map( char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Pair<byte[],Boolean> map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
if ( canUseRead(read) ) {
return getCorrectlyOrientedBaseQualities(read);
} else {

11
java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.BaseUtils;
@ -56,8 +57,8 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateColl
* @param read the read to assess
* @return true if the read can be processed, false if it should be ignored
*/
public boolean filter(char[] ref, SAMRecord read) {
return (read.getCigar().numCigarElements() == 1 && read.getReadLength() <= ref.length && (!useNonNextBestBase || read.getAttribute("SQ") != null));
public boolean filter(ReferenceContext ref, SAMRecord read) {
return (read.getCigar().numCigarElements() == 1 && read.getReadLength() <= ref.getBases().length && (!useNonNextBestBase || read.getAttribute("SQ") != null));
}
/**
@ -71,7 +72,7 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateColl
* Last element is for internal use so the reduce() function can figure out how
* many reads we processed.
*/
public boolean[] map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public boolean[] map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
boolean[] errorsPerCycle = new boolean[read.getReadLength() + 1];
byte[] bases = read.getReadBases();
@ -85,7 +86,7 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateColl
System.out.println();
for (int cycle = 0; cycle < bases.length; cycle++) {
byte compBase = convertIUPACBaseToSimpleBase((byte)ref[cycle]);
byte compBase = convertIUPACBaseToSimpleBase(ref.getBases()[cycle]);
System.out.print((char) compBase);
}
@ -93,7 +94,7 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateColl
}
for (int cycle = 0; cycle < bases.length; cycle++) {
byte compBase = convertIUPACBaseToSimpleBase((byte)ref[cycle]);
byte compBase = convertIUPACBaseToSimpleBase(ref.getBases()[cycle]);
if (compBase != '.') {
if (useNextBestBase || useNextRandomBase || useNonNextBestBase) {

3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadQualityScoreWalker.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
@ -70,7 +71,7 @@ public class ReadQualityScoreWalker extends ReadWalker<SAMRecord, SAMFileWriter>
protected static BufferedReader inputReader = null;
protected static String line = null;
public SAMRecord map( char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
return read; // all the work is done in the reduce step for this walker
}

3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReplaceQuals.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.collections.Pair;
import net.sf.samtools.*;
@ -90,7 +91,7 @@ public class ReplaceQuals extends ReadWalker<SAMRecord, SAMFileWriter> {
/**
*
*/
public SAMRecord map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public SAMRecord map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
final String name = read.getReadName();
if ( readNameToPairs.containsKey(name) ) {

3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.alignment.bwa.BWAAligner;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
@ -130,7 +131,7 @@ public class TestReadFishingWalker extends ReadWalker<Integer,Long> {
}
@Override
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
Alignment bestAlignment = aligner.getBestAlignment(read.getReadBases());
System.out.println("bestAlignment = " + bestAlignment);
return 1;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCFReferenceFixerWalker.java
View File

@ -46,7 +46,7 @@ public class VCFReferenceFixerWalker extends RodWalker<VCFRecord,Long> {
vcfrod = (VCFRecord) rod;
}
if (vcfrod != null) vcfrod.setReferenceBase(new String(BaseUtils.charSeq2byteSeq(context.getBases())));
if (vcfrod != null) vcfrod.setReferenceBase(new String(context.getBases()));
return vcfrod;
/*

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java
View File

@ -62,7 +62,7 @@ public class ProportionOfNonrefBasesSupportingSNP implements InfoFieldAnnotation
Pair<Integer,Integer> totalNonref_totalSNP = new Pair<Integer,Integer>(0,0);
for ( String sample : context.keySet() ) {
ReadBackedPileup pileup = context.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
totalNonref_totalSNP = getNonrefAndSNP(pileup, ref.getBase(), vc.getAlternateAllele(0).toString().charAt(0), totalNonref_totalSNP);
totalNonref_totalSNP = getNonrefAndSNP(pileup, ref.getBaseAsChar(), vc.getAlternateAllele(0).toString().charAt(0), totalNonref_totalSNP);
}
if ( totalNonref_totalSNP.equals(new Pair<Integer,Integer>(0,0)) )

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java
View File

@ -59,7 +59,7 @@ public class ProportionOfRefSecondBasesSupportingSNP implements InfoFieldAnnotat
Pair<Integer,Integer> totalAndSNPSupporting = new Pair<Integer,Integer>(0,0);
for ( String sample : context.keySet() ) {
ReadBackedPileup pileup = context.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
totalAndSNPSupporting = getTotalRefAndSNPSupportCounts(pileup, ref.getBase(), vc.getAlternateAllele(0).toString().charAt(0), totalAndSNPSupporting);
totalAndSNPSupporting = getTotalRefAndSNPSupportCounts(pileup, ref.getBaseAsChar(), vc.getAlternateAllele(0).toString().charAt(0), totalAndSNPSupporting);
}
if ( totalAndSNPSupporting.equals(new Pair<Integer,Integer>(0,0)) )

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java
View File

@ -62,7 +62,7 @@ public class ProportionOfSNPSecondBasesSupportingRef implements InfoFieldAnnotat
Pair<Integer,Integer> totalAndSNPSupporting = new Pair<Integer,Integer>(0,0);
for ( String sample : context.keySet() ) {
ReadBackedPileup pileup = context.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
totalAndSNPSupporting = getTotalSNPandRefSupporting(pileup, ref.getBase(), vc.getAlternateAllele(0).toString().charAt(0), totalAndSNPSupporting);
totalAndSNPSupporting = getTotalSNPandRefSupporting(pileup, ref.getBaseAsChar(), vc.getAlternateAllele(0).toString().charAt(0), totalAndSNPSupporting);
}
if ( totalAndSNPSupporting.equals(new Pair<Integer,Integer>(0,0)) )

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/LocusConcordanceInfo.java
View File

@ -54,7 +54,7 @@ class LocusConcordanceInfo {
}
public byte getReferenceBase() {
return (byte) reference.getBase();
return reference.getBase();
}
public boolean isTruthOnly () {
@ -63,7 +63,7 @@ class LocusConcordanceInfo {
public boolean isVariantSite() {
for ( VCFGenotypeRecord g : truthVCFRecord.getVCFGenotypeRecords() ) {
if ( g.isVariant(reference.getBase()) ) {
if ( g.isVariant(reference.getBaseAsChar()) ) {
return true;
}
}

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BeagleTrioToVCFWalker.java
View File

@ -73,7 +73,7 @@ public class BeagleTrioToVCFWalker extends RodWalker<VariantContext, Long> {
VariantContext vc = null;
if ( ref != null ) {
vc = tracker.getVariantContext(TRACK_NAME, null, context.getLocation(), false);
vc = tracker.getVariantContext(ref, TRACK_NAME, null, context.getLocation(), false);
BeagleROD beagle = tracker.lookup(BEAGLE_NAME,BeagleROD.class);
if ( vc != null ) {

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/VCFToBeagleWalker.java
View File

@ -67,7 +67,7 @@ public class VCFToBeagleWalker extends RodWalker<Integer, VCFToBeagleWalker.Resu
if ( ref != null ) {
EnumSet<VariantContext.Type> allowedTypes = EnumSet.of(VariantContext.Type.SNP);
VariantContext vc = tracker.getVariantContext("variants", allowedTypes, context.getLocation(), false);
VariantContext vc = tracker.getVariantContext(ref, "variants", allowedTypes, context.getLocation(), false);
if ( vc != null && vc.isBiallelic() && vc.isNotFiltered() ) {
if ( trio != null ) { // we are emitting a trio file

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.java
View File

@ -28,6 +28,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import java.util.ArrayList;
@ -106,7 +107,7 @@ public class CalculateAlleleLikelihoodsWalker extends ReadWalker<Integer, Intege
return 0;
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
HLAnamesAL.add(read.getReadName());
HLAreadsAL.add(formatter.FormatRead(read.getCigarString(), read.getReadString()));
HLAstartposAL.add(read.getAlignmentStart());

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculatePhaseLikelihoodsWalker.java
View File

@ -29,6 +29,7 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import java.util.ArrayList;
@ -180,7 +181,7 @@ public class CalculatePhaseLikelihoodsWalker extends ReadWalker<Integer, Integer
return isWithinInterval;
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
if (!ReadsToDiscard.contains(read.getReadName())){
UpdateCorrelation(read);
}else{

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
View File

@ -408,7 +408,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
}
//Get likelihood score for homozygous ref: used to normalize likelihoood scores at 0.
String homref = String.valueOf(ref.getBase())+String.valueOf(ref.getBase());
String homref = String.valueOf(ref.getBaseAsChar())+String.valueOf(ref.getBaseAsChar());
Double homreflikelihood = Double.parseDouble((String) Scores.get(homref).toString());
//Add SNP if it is a SNP and hasn't been added before

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/ClusterReadsWalker.java
View File

@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import java.util.ArrayList;
@ -89,7 +90,7 @@ public class ClusterReadsWalker extends ReadWalker<Integer, Integer> {
return 0;
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker tracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
//Calculate concordance for this read and all overlapping reads
if (!ReadsToDiscard.contains(read.getReadName())){
AlignedReads.add(read);

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreateHaplotypesWalker.java
View File

@ -3,6 +3,8 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import java.util.Hashtable;
/**
* Creates a haplotype file given reads (for SNP analysis, imputation, etc)
@ -37,7 +39,7 @@ public class CreateHaplotypesWalker extends ReadWalker<Integer, Integer> {
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
int readstart = read.getAlignmentStart();
int readstop = read.getAlignmentEnd();

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java
View File

@ -28,6 +28,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import java.util.ArrayList;
@ -209,7 +210,7 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
}
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
HLAnamesAL.add(read.getReadName());
HLAreadsAL.add(formatter.FormatRead(read.getCigarString(), read.getReadString()));
HLAstartposAL.add(read.getAlignmentStart());

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java
View File

@ -28,6 +28,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import java.util.ArrayList;
@ -227,7 +228,7 @@ public class FindClosestAlleleWalker extends ReadWalker<Integer, Integer> {
return maxFreq;
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
//Calculate concordance for this read and all overlapping reads
if (read.getMappingQuality() > 0){
double maxConcordance = CalculateConcordance(read);

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindPolymorphicSitesWalker.java
View File

@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import java.util.ArrayList;
@ -139,7 +140,7 @@ public class FindPolymorphicSitesWalker extends ReadWalker<Integer, Integer> {
NonPolymorphicSites = nonpolymorphicsites.toArray(new Integer[nonpolymorphicsites.size()]);
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
//Calculate concordance for this read and all overlapping reads
return 1;
}

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/ImputeAllelesWalker.java
View File

@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import java.io.FileInputStream;
import java.io.BufferedReader;
@ -161,7 +162,7 @@ public class ImputeAllelesWalker extends ReadWalker<Integer, Integer> {
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
int readstart = read.getAlignmentStart();
int readstop = read.getAlignmentEnd();
int startimputation = 0, stopimputation = 0;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
View File

@ -125,7 +125,7 @@ public class LocusMismatchWalker extends LocusWalker<String,Integer> implements
//System.out.printf("Using %s%n", e.getRead().getReadName());
baseCounts[e.getBaseIndex()] += 1;
usableDepth++;
if ( ! BaseUtils.basesAreEqual(e.getBase(), (byte)ref.getBase()) ) {
if ( ! BaseUtils.basesAreEqual(e.getBase(), ref.getBase()) ) {
nMismatches++;
qSumMismatches += e.getQual();
}
@ -138,7 +138,7 @@ public class LocusMismatchWalker extends LocusWalker<String,Integer> implements
baseCountString += baseCounts[BaseUtils.simpleBaseToBaseIndex(b)] + " ";
}
return String.format("%s %c %10s %5.2f %d %d %d %s",
pileup.getLocation(), ref.getBase(),
pileup.getLocation(), ref.getBaseAsChar(),
getGenotypeClass(g), 10 * g.getNegLog10PError(),
usableDepth, nMismatches, qSumMismatches, baseCountString);
}

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
View File

@ -90,7 +90,7 @@ public class TrioGenotyperWalker extends RefWalker<VariantContext, Integer>{
}
public VariantContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
VariantContext vc = tracker.getVariantContext("variants", EnumSet.of(VariantContext.Type.SNP), context.getLocation(), true);
VariantContext vc = tracker.getVariantContext(ref, "variants", EnumSet.of(VariantContext.Type.SNP), context.getLocation(), true);
if ( vc != null && vc.isPolymorphic() ) {
if ( ! vc.hasGenotypes(FAMILY_MEMBERS) )
@ -179,7 +179,7 @@ public class TrioGenotyperWalker extends RefWalker<VariantContext, Integer>{
if ( a == 0 )
writer.writeHeader(VariantContextAdaptors.createVCFHeader(null, vc));
writer.addRecord(VariantContextAdaptors.toVCF(vc, '.'));
writer.addRecord(VariantContextAdaptors.toVCF(vc, (byte)'.'));
a++;
}

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/VCFConcordance.java
View File

@ -31,8 +31,8 @@ public class VCFConcordance extends RodWalker<Integer, Integer> {
VariantContext eval = null;
VariantContext truth = null;
try {
eval = tracker.getVariantContext("eval", vc, loc, true);
truth = tracker.getVariantContext("truth", vc, loc, true);
eval = tracker.getVariantContext(ref, "eval", vc, loc, true);
truth = tracker.getVariantContext(ref, "truth", vc, loc, true);
} catch (java.util.NoSuchElementException e) {
return 0;
}

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
View File

@ -205,11 +205,11 @@ public class GenomicAnnotator extends RodWalker<Integer, Integer> {
return 0;
Object variant = rods.get(0);
if( ref.getBase() == 'N') {
if( BaseUtils.isNBase(ref.getBase()) ) {
return 0; //TODO Currently, VariantContextAdaptors.toVCF(annotatedVC, ref.getBase()) fails when base is 'N'. is this right?
}
VariantContext vc = VariantContextAdaptors.toVariantContext("variant", variant);
VariantContext vc = VariantContextAdaptors.toVariantContext("variant", variant, ref);
if ( vc == null )
return 0;

8
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java
View File

@ -261,7 +261,7 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
if(parsedTranscriptRod.positiveStrand) {
parsedTranscriptRod.txSequence.append(ref.getBase());
} else {
final char complementBase = BaseUtils.simpleComplement(ref.getBase());
final char complementBase = BaseUtils.simpleComplement(ref.getBaseAsChar());
parsedTranscriptRod.txSequence.insert(0, complementBase);
}
@ -275,16 +275,16 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
{
if(position < parsedTranscriptRod.cdsStart)
{
parsedTranscriptRod.utr5Sequence.append(ref.getBase()); //within utr5
parsedTranscriptRod.utr5Sequence.append(ref.getBaseAsChar()); //within utr5
}
else if(position >= parsedTranscriptRod.cdsStart && position <= parsedTranscriptRod.cdsEnd)
{
parsedTranscriptRod.cdsSequence.append(ref.getBase()); //within CDS
parsedTranscriptRod.cdsSequence.append(ref.getBaseAsChar()); //within CDS
}
}
else
{
final char complementBase = BaseUtils.simpleComplement(ref.getBase());
final char complementBase = BaseUtils.simpleComplement(ref.getBaseAsChar());
if(position > parsedTranscriptRod.cdsEnd)
{
//As we move left to right (aka. 3' to 5'), we do insert(0,..) to reverse the sequence so that it become 5' to 3' in parsedTranscriptRod.utr5Sequence.

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java
View File

@ -81,7 +81,7 @@ public class ComputeConfusionMatrix extends LocusWalker<Integer, Integer> {
int windowCenter = (windowLength - 1)/2;
String fwRefBases = new String(ref.getBases());
String fwRefBase = String.format("%c", ref.getBase());
String fwRefBase = String.format("%c", ref.getBaseAsChar());
String fwWindowLeft = fwRefBases.substring(windowCenter - WINDOW_SIZE, windowCenter);
//String rcRefBases = new String(BaseUtils.simpleReverseComplement(ref.getBases()));

5
java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/MatePairLibrarySize.java
View File

@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.diagnostics;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.StingException;
import net.sf.samtools.SAMRecord;
@ -31,11 +32,11 @@ public class MatePairLibrarySize extends ReadWalker<Integer, Integer> {
}
}
public boolean filter(char[] ref, SAMRecord read) {
public boolean filter(ReferenceContext ref, SAMRecord read) {
return (read.getReadPairedFlag() && read.getFirstOfPairFlag());
}
public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
int insert = read.getInferredInsertSize();
Integer oldcount = matePairSize.get(read.getReadGroup().getLibrary()).get(insert);

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java
View File

@ -67,7 +67,7 @@ public class SNPDensity extends RefWalker<Pair<VariantContext, GenomeLoc>, SNPDe
VCFRecord vcf = tracker.lookup("eval",VCFRecord.class);
if (vcf != null)
vc = VariantContextAdaptors.toVariantContext("eval", vcf);
vc = VariantContextAdaptors.toVariantContext("eval", vcf, ref);
return new Pair<VariantContext, GenomeLoc>(vc, context.getLocation());
}

5
java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceAssessor.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.graphalign;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.commandline.Argument;
@ -176,7 +177,7 @@ public class GraphReferenceAssessor extends ReadWalker<Integer, Integer> {
return minNMM;
}
public Integer map(char[] refArg, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext refArg, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
if ( MAXREADS-- == 0 ) {
System.exit(0);
@ -184,7 +185,7 @@ public class GraphReferenceAssessor extends ReadWalker<Integer, Integer> {
;
} else if ( ! read.getReadUnmappedFlag() && read.getCigar().numCigarElements() == 1 ) {
try {
byte[] ref = BaseUtils.charSeq2byteSeq(refArg);
byte[] ref = refArg.getBases();
// we're all XM
int nMMFromRead = (Short)read.getAttribute("NM");
MismatchCounter nAlignedMM = countMismatches(ref, read.getReadBases(), read.getBaseQualities());

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java
View File

@ -68,7 +68,7 @@ public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> impleme
if (ref.getBase() == 'N' || ref.getBase() == 'n') return null; // we don't deal with the N ref base case
ReadBackedPileup pileup = context.getPileup();
double likelihoods[] = DiploidGenotypePriors.getReferencePolarizedPriors(ref.getBase(),
double likelihoods[] = DiploidGenotypePriors.getReferencePolarizedPriors(ref.getBaseAsChar(),
DiploidGenotypePriors.HUMAN_HETEROZYGOSITY,
0.01);
// get the bases and qualities from the pileup
@ -97,7 +97,7 @@ public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> impleme
return new SimpleCall(context.getLocation(),
GENOTYPE.values()[sortedList[9]].toString(),
likelihoods[sortedList[9]] - likelihoods[sortedList[8]],
ref.getBase());
ref.getBaseAsChar());
}
/**

12
java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java
View File

@ -39,14 +39,14 @@ public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Int
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
char refBase = Character.toUpperCase(ref.getBase());
char refBase = Character.toUpperCase(ref.getBaseAsChar());
ReadBackedPileup pileup = context.getBasePileup();
int[] baseCounts = pileup.getBaseCounts();
int length = 0;
for (int i : baseCounts) {length += i;}
char[] contextBases = ref.getBases();
char prevBase = Character.toUpperCase(contextBases[0]);
char nextBase = Character.toUpperCase(contextBases[contextBases.length - 1]);
byte[] contextBases = ref.getBases();
byte prevBase = (byte)Character.toUpperCase(contextBases[0]);
byte nextBase = (byte)Character.toUpperCase(contextBases[contextBases.length - 1]);
if (contextBases.length == 3 && refBase != 'N' && pileup.getBases() != null && pileup.getSecondaryBases() != null) {
VariantCallContext ugResult = ug.runGenotyper(tracker,ref,context);
@ -83,14 +83,14 @@ public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Int
if (!element.getRead().getReadNegativeStrandFlag()) {
strandRef = Character.toString(refBase);
strandPrimary = Character.toString(primaryBase);
strandPrev = Character.toString(prevBase);
strandPrev = Character.toString((char)prevBase);
strandSecondary = Character.toString(secondaryBase);
strandCall = call;
}
else {
strandRef = Character.toString(BaseUtils.simpleComplement(refBase));
strandPrimary = Character.toString(BaseUtils.simpleComplement(primaryBase));
strandPrev = Character.toString(BaseUtils.simpleComplement(nextBase));
strandPrev = Character.toString(BaseUtils.simpleComplement((char)nextBase));
strandSecondary = Character.toString(BaseUtils.simpleComplement(secondaryBase));
strandCall = BaseUtils.simpleReverseComplement(call);
}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
View File

@ -54,7 +54,7 @@ public class AnnotationDataManager {
INDICATE_MEAN_NUM_VARS = _INDICATE_MEAN_NUM_VARS;
}
public void addAnnotations( final VariantContext vc, final char ref, final String sampleName, final boolean isInTruthSet, final boolean isTrueVariant ) {
public void addAnnotations( final VariantContext vc, final byte ref, final String sampleName, final boolean isInTruthSet, final boolean isTrueVariant ) {
if( sampleName != null ) { // Only process variants that are found in the sample with this sampleName
if( vc.getGenotype(sampleName).isNoCall() ) { // This variant isn't found in this sample so break out

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/ApplyVariantClustersWalker.java
View File

@ -172,7 +172,7 @@ public class ApplyVariantClustersWalker extends RodWalker<ExpandingArrayList<Var
boolean isKnown = !vc.getAttribute("ID").equals(".");
if(usingDBSNP) {
isKnown = false;
for( VariantContext dbsnpVC : tracker.getVariantContexts(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, null, context.getLocation(), false, false) ) {
for( VariantContext dbsnpVC : tracker.getVariantContexts(ref, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, null, context.getLocation(), false, false) ) {
if(dbsnpVC != null && dbsnpVC.isSNP()) {
isKnown=true;
}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizer.java
View File

@ -146,7 +146,7 @@ public class VariantOptimizer extends RodWalker<ExpandingArrayList<VariantDatum>
boolean isKnown = !vc.getAttribute("ID").equals(".");
if(usingDBSNP) {
isKnown = false;
for( final VariantContext dbsnpVC : tracker.getVariantContexts(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, null, context.getLocation(), false, false) ) {
for( final VariantContext dbsnpVC : tracker.getVariantContexts(ref, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, null, context.getLocation(), false, false) ) {
if(dbsnpVC != null && dbsnpVC.isSNP()) {
isKnown = true;
}

2
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
View File

@ -89,7 +89,7 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
if ( mHeader == null )
throw new IllegalStateException("The VCF Header must be written before records can be added");
VCFRecord call = VariantContextAdaptors.toVCF(vc, refAllele.charAt(0), allowedGenotypeFormatStrings, false, false);
VCFRecord call = VariantContextAdaptors.toVCF(vc, (byte)refAllele.charAt(0), allowedGenotypeFormatStrings, false, false);
Set<Allele> altAlleles = vc.getAlternateAlleles();
StringBuffer altAlleleCountString = new StringBuffer();

4
java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
View File

@ -346,7 +346,7 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
* @return list of distinct events; first element of a pair is a string representation of the event, second element
* gives the number of reads, in which that event was observed
*/
public List<Pair<String,Integer>> getEventStringsWithCounts(char[] refBases) {
public List<Pair<String,Integer>> getEventStringsWithCounts(byte[] refBases) {
Map<String, Integer> events = new HashMap<String,Integer>();
for ( ExtendedEventPileupElement e : this ) {
@ -385,7 +385,7 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
* @param refBases
* @return
*/
private String getDeletionString(int length, char[] refBases) {
private String getDeletionString(int length, byte[] refBases) {
if ( refBases == null ) {
return Integer.toString(length)+"D"; // if we do not have reference bases, we can only report something like "5D"
} else {

4
java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
View File

@ -156,7 +156,7 @@ public class AlignmentUtils {
int windowStart = (int)ref.getWindow().getStart();
int windowStop = (int)ref.getWindow().getStop();
char[] refBases = ref.getBases();
byte[] refBases = ref.getBases();
byte[] readBases = p.getRead().getReadBases();
byte[] readQualities = p.getRead().getBaseQualities();
Cigar c = p.getRead().getCigar();
@ -179,7 +179,7 @@ public class AlignmentUtils {
if ( currentPos < windowStart )
continue;
char refChr = refBases[refIndex++];
byte refChr = refBases[refIndex++];
// do we need to skip the target site?
if ( ignoreTargetSite && ref.getLocus().getStart() == currentPos )

5
java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java
View File

@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.apache.log4j.Logger;
import net.sf.samtools.SAMRecord;
@ -102,14 +103,14 @@ public class ArtificialReadsTraversal<M,T> extends TraversalEngine<M,T,Walker<M,
AlignmentContext alignment = null;
// an array of characters that represent the reference
char[] refSeq = null;
ReferenceContext refSeq = null;
// update the number of reads we've seen
TraversalStatistics.nRecords++;
final boolean keepMeP = readWalker.filter(refSeq, read);
if (keepMeP) {
M x = readWalker.map(refSeq, read,null); // TODO: fix me at some point, it would be nice to fake out ROD data too
M x = readWalker.map(refSeq, read, null); // TODO: fix me at some point, it would be nice to fake out ROD data too
sum = readWalker.reduce(x, sum);
}

5
java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java
View File

@ -61,7 +61,8 @@ public class LocusReferenceViewUnitTest extends ReferenceViewTemplate {
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, shard.getGenomeLocs().get(0), null, sequenceFile, null);
LocusReferenceView view = new LocusReferenceView(dataProvider);
char[] results = view.getReferenceBases(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length() + 9));
byte[] results = view.getReferenceBases(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length() + 9));
System.out.printf("results are %s%n", new String(results));
Assert.assertEquals(20, results.length);
for (int x = 0; x < results.length; x++) {
if (x <= 10) Assert.assertTrue(results[x] != 'X');
@ -104,7 +105,7 @@ public class LocusReferenceViewUnitTest extends ReferenceViewTemplate {
ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(locus.getContig(), locus.getStart(), locus.getStop());
char expected = StringUtil.bytesToString(expectedAsSeq.getBases()).charAt(0);
char actual = view.getReferenceContext(locus).getBase();
char actual = view.getReferenceContext(locus).getBaseAsChar();
Assert.assertEquals(String.format("Value of base at position %s in shard %s does not match expected", locus.toString(), shard.getGenomeLocs()),
expected,

9
java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java
View File

@ -75,8 +75,9 @@ public class ReadReferenceViewUnitTest extends ReferenceViewTemplate {
SAMRecord rec = buildSAMRecord(selectedContig.getSequenceName(),(int)contigStart,(int)contigStop);
ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(selectedContig.getSequenceName(),(int)contigStart,selectedContig.getSequenceLength());
char[] expected = StringUtil.bytesToString(expectedAsSeq.getBases()).toCharArray();
char[] actual = view.getReferenceBases(rec);
//char[] expected = StringUtil.bytesToString(expectedAsSeq.getBases()).toCharArray();
byte[] expected = expectedAsSeq.getBases();
byte[] actual = view.getReferenceBases(rec);
Assert.assertEquals(expected.length, (readLength - overlap));
Assert.assertEquals(actual.length, readLength);
@ -101,8 +102,8 @@ public class ReadReferenceViewUnitTest extends ReferenceViewTemplate {
ReadReferenceView view = new ReadReferenceView(dataProvider);
ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(loc.getContig(),loc.getStart(),loc.getStop());
char[] expected = StringUtil.bytesToString(expectedAsSeq.getBases()).toCharArray();
char[] actual = view.getReferenceBases(read);
byte[] expected = expectedAsSeq.getBases();
byte[] actual = view.getReferenceBases(read);
Assert.assertArrayEquals(String.format("Base array at in shard %s does not match expected",loc.toString()),
expected,

6
java/test/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptorsUnitTest.java
View File

@ -84,7 +84,7 @@ public class VariantContextAdaptorsUnitTest extends BaseTest {
while (glf.hasNext()) {
glf.next();
records.add((GLFSingleCall)glf.mRecord); // we know they're all single calls in the reference file
VariantContext vc = VariantContextAdaptors.toVariantContext("GLF",glf);
VariantContext vc = VariantContextAdaptors.toVariantContext("GLF",glf, null);
gw.addCall(vc,null);
}
gw.close(); // close the file
@ -148,7 +148,7 @@ public class VariantContextAdaptorsUnitTest extends BaseTest {
while (line != null && line != "") {
geliText = (GeliTextFeature)codec.decode(line);
records.add(geliText); // we know they're all single calls in the reference file
VariantContext vc = VariantContextAdaptors.toVariantContext("Geli",geliText);
VariantContext vc = VariantContextAdaptors.toVariantContext("Geli",geliText, null);
if (vc != null) gw.addCall(vc,null);
line = readLine(reader);
}
@ -211,7 +211,7 @@ public class VariantContextAdaptorsUnitTest extends BaseTest {
while (iterator.hasNext()) {
rodGELI gel = new rodGELI("myROD",iterator.next());
records.add(gel);
VariantContext vc = VariantContextAdaptors.toVariantContext("myROD",gel);
VariantContext vc = VariantContextAdaptors.toVariantContext("myROD",gel, null);
if (vc != null) gw.addCall(vc,null);
}
iterator.close();

5
java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerUnitTest.java
View File

@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.datasources.shards.Shard;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.sam.ArtificialReadsTraversal;
import org.broadinstitute.sting.utils.sam.ArtificialSAMFileWriter;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
@ -54,7 +55,9 @@ public class PrintReadsWalkerUnitTest extends BaseTest {
*/
private ArtificialReadsTraversal trav;
private int readTotal = 0;
private char bases[] = {'a', 't'};
//private char bases[] = {'a', 't'};
private ReferenceContext bases = null;
//private ReferenceContext ref = new ReferenceContext()
@Before
public void before() {