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option to print out the indels found by the cleaner to a file 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@709 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-05-14 17:50:08 +00:00
parent b62bddee42
commit 7a1f85ff86
1 changed files with 36 additions and 5 deletions
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41
java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java
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@ -14,6 +14,7 @@ import net.sf.samtools.*;
import java.util.*;
import java.io.File;
import java.io.FileWriter;
@WalkerName("IntervalCleaner")
public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer> {
@ -21,18 +22,30 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
public int maxReadLength = -1;
@Argument(fullName="OutputCleaned", shortName="O", required=true, doc="Output file (sam or bam) for improved (realigned) reads")
public String OUT;
@Argument(fullName="OutputIndels", shortName="indels", required=false, doc="Output file (text) for the indels found")
public String OUT_INDELS = null;
@Argument(fullName="OutputAllReads", shortName="all", doc="print out all reads (otherwise, just those within the intervals)", required=false)
public boolean printAllReads = false;
public static final int MAX_QUAL = 99;
private SAMFileWriter writer;
private FileWriter indelOutput = null;
// we need to sort the reads ourselves because SAM headers get messed up and claim to be "unsorted" sometimes
private TreeSet<ComparableSAMRecord> readsToWrite;
public void initialize() {
SAMFileHeader header = getToolkit().getSamReader().getFileHeader();
SAMFileHeader header = getToolkit().getEngine().getSAMHeader();
writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, new File(OUT));
if ( OUT_INDELS != null ) {
try {
indelOutput = new FileWriter(new File(OUT_INDELS));
} catch (Exception e) {
err.println(e.getMessage());
indelOutput = null;
}
}
readsToWrite = new TreeSet<ComparableSAMRecord>();
}
@ -82,6 +95,13 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
public void onTraversalDone(Integer result) {
out.println("Saw " + result + " intervals");
writer.close();
if ( OUT_INDELS != null ) {
try {
indelOutput.close();
} catch (Exception e) {
err.println(e.getMessage());
}
}
}
private static int mismatchQualitySum(AlignedRead aRead, String ref, int refIndex) {
@ -205,6 +225,17 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// if the best alternate consensus has a smaller sum of quality score mismatches, then clean!
if ( bestConsensus != null && bestConsensus.mismatchSum < totalMismatchSum ) {
logger.info("CLEAN: " + bestConsensus.str);
if ( indelOutput != null && bestConsensus.cigar.numCigarElements() > 1 ) {
StringBuffer str = new StringBuffer();
str.append(reads.get(0).getReferenceName());
int position = bestConsensus.positionOnReference + bestConsensus.cigar.getCigarElement(0).getLength();
str.append(":" + (leftmostIndex + position));
CigarElement ce = bestConsensus.cigar.getCigarElement(1);
str.append(" " + ce.getLength() + ce.getOperator() + "\n");
try {
indelOutput.write(str.toString());
} catch (Exception e) {}
}
// clean the appropriate reads
for ( Pair<Integer, Integer> indexPair : bestConsensus.readIndexes )
@ -571,10 +602,10 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
for ( int i = 0 ; i < cig.numCigarElements() ; i++ ) {
char c='?';
switch ( cig.getCigarElement(i).getOperator() ) {
case M : c = 'M'; break;
case D : c = 'D'; break;
case I : c = 'I'; break;
switch ( cig.getCigarElement(i).getOperator() ) {
case M : c = 'M'; break;
case D : c = 'D'; break;
case I : c = 'I'; break;
}
b.append(cig.getCigarElement(i).getLength());
b.append(c);