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Added option to output the locations of indels in the alternate reference 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1424 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-16 03:46:36 +00:00
parent 4b6ddc55bd
commit d4808433a1
2 changed files with 40 additions and 2 deletions
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35
java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
View File

@ -7,8 +7,10 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import java.io.*;
import java.util.Iterator;
// create a fasta sequence file from a reference, intervals, and rod(s) of variants
// if there are multiple variants at a site, we take the first one seen
@ -20,8 +22,23 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
private Boolean MASK_SNPS = false;
@Argument(fullName="outputSequenomFormat", shortName="sequenom", doc="output results in sequenom format (overrides 'maskSNPs' argument)", required=false)
private Boolean SEQUENOM = false;
@Argument(fullName="outputIndelPositions", shortName="indels", doc="output the positions of the indels in the new reference", required=false)
String indelsFile = null;
int deletionBasesRemaining = 0;
private int deletionBasesRemaining = 0;
private long basesSeen = 0;
private PrintWriter indelsWriter = null;
public void initialize() {
super.initialize();
if ( indelsFile != null ) {
try {
indelsWriter = new PrintWriter(indelsFile);
} catch (IOException e) {
throw new RuntimeException("Unable to open indel positions output file: " + indelsFile);
}
}
}
public Pair<GenomeLoc, String> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
String refBase = String.valueOf(ref.getBase());
@ -41,16 +58,32 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
AllelicVariant variant = (AllelicVariant)rod;
if ( variant.isDeletion() ) {
deletionBasesRemaining = variant.length();
basesSeen++;
if ( indelsWriter != null )
indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.length()));
// delete the next n bases, not this one
return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[-/") : refBase));
} else if ( variant.isInsertion() ) {
basesSeen++;
if ( indelsWriter != null )
indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.length()));
basesSeen += variant.length();
return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[+/"+variant.getAltBasesFWD()+"]") : refBase.concat(variant.getAltBasesFWD())));
} else if ( variant.isSNP() ) {
basesSeen++;
return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM || MASK_SNPS ? "N" : variant.getAltBasesFWD()));
}
}
// if we got here then we're just ref
basesSeen++;
return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
}
public void onTraversalDone(GenomeLoc sum) {
super.onTraversalDone(sum);
if ( indelsWriter != null )
indelsWriter.close();
}
}

7
java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaSequence.java
View File

@ -25,13 +25,18 @@ public class FastaSequence {
public void flush() {
printFasta(true);
printedHeader = false;
sequenceCounter++;
}
public String getCurrentID() {
return String.valueOf(sequenceCounter);
}
private void printFasta(boolean printAll) {
if ( sb.length() == 0 || (!printAll && sb.length() < 60) )
return;
if ( !printedHeader ) {
out.println(">" + sequenceCounter++);
out.println(">" + sequenceCounter);
printedHeader = true;
}
int lines = sb.length() / 60;