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Parallel FlagStat

This commit is contained in:
Mark DePristo 2012-08-25 17:19:57 -04:00
parent af540888f1
commit 5066b14335
1 changed files with 69 additions and 42 deletions
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111
public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java
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@ -45,12 +45,12 @@ import java.text.NumberFormat;
*/ */
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) @DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS}) @Requires({DataSource.READS})
public class FlagStat extends ReadWalker<Integer, Integer> { public class FlagStat extends ReadWalker<FlagStat.FlagStatus, FlagStat.FlagStatus> implements TreeReducible<FlagStat.FlagStatus> {
@Output @Output
PrintStream out; PrintStream out;
// what comes out of the flagstat // what comes out of the flagstat
static class FlagStatus { public final static class FlagStatus {
long readCount = 0L; long readCount = 0L;
long QC_failure = 0L; long QC_failure = 0L;
long duplicates = 0L; long duplicates = 0L;
@ -117,62 +117,89 @@ public class FlagStat extends ReadWalker<Integer, Integer> {
return builder.toString(); return builder.toString();
} }
} public FlagStatus add(final FlagStatus other) {
readCount += other.readCount;
QC_failure += other.QC_failure;
duplicates += other.duplicates;
mapped += other.mapped;
paired_in_sequencing += other.paired_in_sequencing;
read1 += other.read1;
read2 += other.read2;
properly_paired += other.properly_paired;
with_itself_and_mate_mapped += other.with_itself_and_mate_mapped;
singletons += other.singletons;
with_mate_mapped_to_a_different_chr += other.with_mate_mapped_to_a_different_chr;
with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5 += other.with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5;
return this;
private FlagStatus myStat = new FlagStatus();
public Integer map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) {
myStat.readCount++;
if (read.getReadFailsVendorQualityCheckFlag()) {
myStat.QC_failure++;
} }
if (read.getDuplicateReadFlag()) {
myStat.duplicates++;
}
if (!read.getReadUnmappedFlag()) {
myStat.mapped++;
}
if (read.getReadPairedFlag()) {
myStat.paired_in_sequencing++;
if (read.getSecondOfPairFlag()) { public FlagStatus add(final GATKSAMRecord read) {
myStat.read2++; this.readCount++;
} else if (read.getReadPairedFlag()) {
myStat.read1++; if (read.getReadFailsVendorQualityCheckFlag()) {
this.QC_failure++;
} }
if (read.getProperPairFlag()) { if (read.getDuplicateReadFlag()) {
myStat.properly_paired++; this.duplicates++;
} }
if (!read.getReadUnmappedFlag() && !read.getMateUnmappedFlag()) { if (!read.getReadUnmappedFlag()) {
myStat.with_itself_and_mate_mapped++; this.mapped++;
}
if (read.getReadPairedFlag()) {
this.paired_in_sequencing++;
if (!read.getReferenceIndex().equals(read.getMateReferenceIndex())) { if (read.getSecondOfPairFlag()) {
myStat.with_mate_mapped_to_a_different_chr++; this.read2++;
} else if (read.getReadPairedFlag()) {
this.read1++;
}
if (read.getProperPairFlag()) {
this.properly_paired++;
}
if (!read.getReadUnmappedFlag() && !read.getMateUnmappedFlag()) {
this.with_itself_and_mate_mapped++;
if (read.getMappingQuality() >= 5) { if (!read.getReferenceIndex().equals(read.getMateReferenceIndex())) {
myStat.with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5++; this.with_mate_mapped_to_a_different_chr++;
if (read.getMappingQuality() >= 5) {
this.with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5++;
}
} }
} }
if (!read.getReadUnmappedFlag() && read.getMateUnmappedFlag()) {
this.singletons++;
}
} }
if (!read.getReadUnmappedFlag() && read.getMateUnmappedFlag()) {
myStat.singletons++; return this;
}
} }
return 1;
} }
public Integer reduceInit() {
return 0; @Override
public FlagStatus map( final ReferenceContext ref, final GATKSAMRecord read, final ReadMetaDataTracker metaDataTracker ) {
return new FlagStatus().add(read);
}
@Override
public FlagStatus reduceInit() {
return new FlagStatus();
} }
public Integer reduce(Integer value, Integer sum) { @Override
return value + sum; public FlagStatus reduce(final FlagStatus value, final FlagStatus sum) {
return sum.add(value);
} }
public void onTraversalDone(Integer result) { @Override
//out.println("[REDUCE RESULT] Traversal result is: " + result); public FlagStatus treeReduce(final FlagStatus value, final FlagStatus sum) {
out.println(myStat.toString()); return sum.add(value);
}
@Override
public void onTraversalDone(final FlagStatus result) {
out.println(result.toString());
} }
} }