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