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Remove some copied code to make sure the traversal engine stays in sync with the locus context provider. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@463 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-04-17 16:41:56 +00:00
parent df5aae5ed4
commit d639ec3776
2 changed files with 3 additions and 40 deletions
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41
java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusContextProvider.java
View File

@ -8,6 +8,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.iterators.LocusIterator; import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import org.broadinstitute.sting.gatk.iterators.LocusIteratorByHanger; import org.broadinstitute.sting.gatk.iterators.LocusIteratorByHanger;
import org.broadinstitute.sting.gatk.traversals.TraversalStatistics; import org.broadinstitute.sting.gatk.traversals.TraversalStatistics;
import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import java.util.ArrayList; import java.util.ArrayList;
@ -30,7 +31,7 @@ public class LocusContextProvider {
protected static Logger logger = Logger.getLogger(LocusContextProvider.class); protected static Logger logger = Logger.getLogger(LocusContextProvider.class);
public LocusContextProvider( Iterator<SAMRecord> reads ) { public LocusContextProvider( Iterator<SAMRecord> reads ) {
this.reads = new FilteringIterator(reads, new locusStreamFilterFunc()); this.reads = new FilteringIterator(reads, new TraversalEngine.locusStreamFilterFunc());
// prepare the iterator by loci from reads // prepare the iterator by loci from reads
loci = new LocusIteratorByHanger(this.reads); loci = new LocusIteratorByHanger(this.reads);
} }
@ -72,42 +73,4 @@ public class LocusContextProvider {
return locus; return locus;
} }
/**
* Class to filter out un-handle-able reads from the stream. We currently are skipping
* unmapped reads, non-primary reads, unaligned reads, and those with indels. We should
* really change this to handle indel containing reads.
* TODO: Update TraversalEngine with our runtime stats.
*/
private class locusStreamFilterFunc implements SamRecordFilter {
SAMRecord lastRead = null;
public boolean filterOut(SAMRecord rec) {
boolean result = false;
String why = "";
if (rec.getReadUnmappedFlag()) {
TraversalStatistics.nUnmappedReads++;
result = true;
why = "Unmapped";
} else if (rec.getNotPrimaryAlignmentFlag()) {
TraversalStatistics.nNotPrimary++;
result = true;
why = "Not Primary";
} else if (rec.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START) {
TraversalStatistics.nBadAlignments++;
result = true;
why = "No alignment start";
}
else {
result = false;
}
if (result) {
//nSkippedReads++;
//System.out.printf(" [filter] %s => %b %s", rec.getReadName(), result, why);
} else {
//nReads++;
}
return result;
}
}
} }

2
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
View File

@ -474,7 +474,7 @@ public abstract class TraversalEngine {
* unmapped reads, non-primary reads, unaligned reads, and those with indels. We should * unmapped reads, non-primary reads, unaligned reads, and those with indels. We should
* really change this to handle indel containing reads. * really change this to handle indel containing reads.
*/ */
class locusStreamFilterFunc implements SamRecordFilter { public static class locusStreamFilterFunc implements SamRecordFilter {
SAMRecord lastRead = null; SAMRecord lastRead = null;
public boolean filterOut(SAMRecord rec) { public boolean filterOut(SAMRecord rec) {
boolean result = false; boolean result = false;