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added method indelPileup. Generates a pileup of indel alleles given reads and ofsets (as from a locus walker). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@663 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-05-12 15:08:24 +00:00
parent ee9077fc69
commit 11723fbcc2
1 changed files with 58 additions and 1 deletions
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59
java/src/org/broadinstitute/sting/utils/BasicPileup.java
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@ -1,7 +1,7 @@
package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.gatk.LocusContext;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.*;
import java.util.List;
import java.util.ArrayList;
@ -226,6 +226,63 @@ abstract public class BasicPileup implements Pileup {
return distString;
}
public static String[] indelPileup( List<SAMRecord> reads, List<Integer> offsets )
{
String[] indels = new String[reads.size()];
for (int i = 0; i < reads.size(); i++)
{
SAMRecord read = reads.get(i);
Cigar cigar = read.getCigar();
int offset = offsets.get(i);
String cigar_string = read.getCigarString();
if (! (cigar_string.contains("I") || cigar_string.contains("D"))) { indels[i] = "null"; continue; }
//System.out.printf("%s:%d %s %s %s ", read.getReferenceName(), read.getAlignmentStart(), read.getReadName(), read.getReadString(), cigar_string);
int k = 0;
for (int j = 0; j < cigar.numCigarElements(); j++)
{
CigarOperator operator = cigar.getCigarElement(j).getOperator();
int length = cigar.getCigarElement(j).getLength();
if (operator == CigarOperator.M)
{
k += length;
}
else if ((k == offset+1) && (operator == CigarOperator.I))
{
// this insertion is associated with this offset (kinda ;) ).
indels[i] = read.getReadString().substring(k, k+length);
//System.out.printf("(I,%d,%d)", k, offset);
break;
}
else if ((k != offset+1) && (operator == CigarOperator.I))
{
//System.out.printf("(i,%d,%d)", k, offset);
k += length;
}
else if ((k == offset) && (operator == CigarOperator.D))
{
// this deletion is associated with this offset.
indels[i] = length + "D";
//System.out.printf("(D,%d,%d)", k, offset);
break;
}
else if (k >= offset)
{
// no indel here.
indels[i] = "null";
//System.out.printf("(N,%d,%d)", k, offset);
break;
}
}
if (indels[i] == null) { indels[i] = "null"; }
//System.out.printf("\n");
}
return indels;
}
public static String pileupDiff(final Pileup a, final Pileup b)
{
return pileupDiff(a,b,true);