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Adjusted Genotype concordance to more accurately use the new Genotyping code, fixed the VCF rod, and temp. fix the build by reintroducing Shermans ReadCigarFormatter 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1745 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-09-29 21:28:21 +00:00
parent 9b78a789e2
commit b1c321f161
3 changed files with 107 additions and 23 deletions
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23
java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
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@ -34,6 +34,12 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
super(name);
}
private RodVCF(String name, VCFRecord currentRecord, VCFReader reader) {
super(name);
mCurrentRecord = currentRecord;
mReader = reader;
}
public void assertNotNull() {
if (mCurrentRecord == null) {
throw new UnsupportedOperationException("The current Record is null");
@ -46,9 +52,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
}
public Object initialize(final File source) throws FileNotFoundException {
if (mReader == null) {
mReader = new VCFReader(source);
}
if (mReader == null) mReader = new VCFReader(source);
return mReader.getHeader();
}
@ -60,7 +64,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
return "";
}
public Iterator<RodVCF> createIterator(String name, File file) {
public static RodVCF createIterator(String name, File file) {
RodVCF vcf = new RodVCF(name);
try {
vcf.initialize(file);
@ -125,7 +129,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
*/
@Override
public boolean isInsertion() {
this.assertNotNull();
this.assertNotNull();
if (!mCurrentRecord.hasAlternateAllele())
return false;
for (String alt : this.mCurrentRecord.getAlternateAlleles()) {
@ -142,7 +146,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
*/
@Override
public boolean isDeletion() {
this.assertNotNull();
this.assertNotNull();
if (!mCurrentRecord.hasAlternateAllele())
return false;
for (String alt : this.mCurrentRecord.getAlternateAlleles()) {
@ -155,7 +159,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
@Override
public GenomeLoc getLocation() {
this.assertNotNull();
return GenomeLocParser.createGenomeLoc(mCurrentRecord.getChromosome(), mCurrentRecord.getPosition());
return GenomeLocParser.createGenomeLoc(mCurrentRecord.getChromosome(), mCurrentRecord.getPosition(), mCurrentRecord.getPosition());
}
/**
@ -202,7 +206,8 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
*/
@Override
public String getAlternateBases() {
if (!this.isBiallelic()) throw new UnsupportedOperationException("We're not biallelic, so please call getAlternateBaseList instead");
if (!this.isBiallelic())
throw new UnsupportedOperationException("We're not biallelic, so please call getAlternateBaseList instead");
return this.mCurrentRecord.getAlternateAlleles().get(0);
}
@ -341,7 +346,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
@Override
public RodVCF next() {
mCurrentRecord = mReader.next();
return this;
return new RodVCF(this.name, mCurrentRecord, mReader);
}
@Override

76
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/ReadCigarFormatter.java 100644
View File

@ -0,0 +1,76 @@
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
/**
* Returns formatted read given read string and cigar string
* Essentially removes header bases, soft clipped bases, and currently removes insertions
* Deletions coded as "D"
*
* @author shermanjia
*/
public class ReadCigarFormatter {
public String FormatRead(String cigar, String read){
// returns a cigar-formatted sequence (removes insertions, inserts 'D' to where deletions occur
String formattedRead = ""; char c; String count;
int cigarPlaceholder = 0; int subcigarLength = 0;
int readPlaceholder = 0; int subreadLength = 0;
//reads cigar string
for (int i = 0; i < cigar.length(); i++){
c = cigar.charAt(i);
if (c == 'M'){
//If reach M for match/mismatch, get number immediately preceeding 'M' and tack on that many characters to sequence
subcigarLength = i-cigarPlaceholder;
count = cigar.substring(cigarPlaceholder, i);
subreadLength = Integer.parseInt(count);
formattedRead = formattedRead + read.substring(readPlaceholder, readPlaceholder+subreadLength);
//increment placeholders
cigarPlaceholder = i+1;
readPlaceholder = readPlaceholder + subreadLength;
} else if (c == 'I'){
//***NOTE: To be modified later if needed (insertions removed here)***
//If reaches I for insertion, get number before 'I' and skip that many characters in sequence
count = cigar.substring(cigarPlaceholder, i);
subreadLength = Integer.parseInt(count);
//increment placeholders without adding inserted bases to sequence (effectively removes insertion).
cigarPlaceholder = i+1;
readPlaceholder = readPlaceholder + subreadLength;
} else if (c == 'H' || c == 'S'){
//(H = Headers or S = Soft clipped removed here)***
//If reaches H for insertion, get number before 'H' and skip that many characters in sequence
count = cigar.substring(cigarPlaceholder, i);
subreadLength = Integer.parseInt(count);
//increment cigar placeholder without adding inserted bases to sequence (effectively removes insertion).
cigarPlaceholder = i+1;
} else if (c == 'D'){
//If reaches D for deletion, insert 'D' into sequence as placeholder
count = cigar.substring(cigarPlaceholder, i);
subreadLength = Integer.parseInt(count);
//Add one 'D' for each deleted base
String deletion = "";
for (int j = 1; j <= subreadLength; j++){
deletion = deletion + "D";
}
//update placeholders
formattedRead = formattedRead + deletion;
cigarPlaceholder = i+1;
}
}
return formattedRead;
}
}

31
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
import org.broadinstitute.sting.utils.genotype.Variation;
@ -50,26 +50,31 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
if ((chip != null && !(chip instanceof VariantBackedByGenotype) || (eval != null && !(eval instanceof VariantBackedByGenotype))))
throw new StingException("Failure: trying to analyze genotypes of non-genotype data");
// This shouldn't happen, but let's check anyways
if ( BaseUtils.simpleBaseToBaseIndex(ref) == -1 )
return;
// This shouldn't happen, but let's check anyways
if (BaseUtils.simpleBaseToBaseIndex(ref) == -1)
return;
// get the genotyping data
Genotype chipGenotype = null;
Genotype evalGenotype = null;
if (chip != null) chipGenotype = ((VariantBackedByGenotype)chip).getCalledGenotype();
if (eval != null) evalGenotype = ((VariantBackedByGenotype)eval).getCalledGenotype();
DiploidGenotype g = DiploidGenotype.createHomGenotype(ref);
int truthIndex, callIndex;
if (chip == null)
truthIndex = UNKNOWN;
else if (chip.getAlternateBases().equals(g.toString()))
else if (!chipGenotype.isVariant(ref))
truthIndex = REF;
else if (chip.getAlternateBases().charAt(0) != chip.getAlternateBases().charAt(1))
else if (chipGenotype.isHet())
truthIndex = VAR_HET;
else
truthIndex = VAR_HOM;
if (eval == null)
callIndex = NO_CALL;
else if (eval.getAlternateBases().equals(g.toString()))
else if (!evalGenotype.isVariant(ref))
callIndex = REF;
else if (eval.getAlternateBases().charAt(0) != eval.getAlternateBases().charAt(1))
else if (evalGenotype.isHet())
callIndex = VAR_HET;
else
callIndex = VAR_HOM;
@ -84,8 +89,8 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
Variation chip = (Variation) tracker.lookup(dbName, null);
if ( eval != null || chip != null )
inc(chip, eval, ref);
if (eval != null || chip != null)
inc(chip, eval, ref);
return null;
}
@ -102,9 +107,7 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
s.add(sb.toString());
}
/**
* How many overall calls where made that aren't NO_CALLS or UNKNOWNS?
*/
/** How many overall calls where made that aren't NO_CALLS or UNKNOWNS? */
private int getNCalled() {
int n = 0;
for (int i = 0; i < 4; i++)