The flagStatReadWalker generates the exact same statistical output as the samtools flagstat command, so the two outputs can be diff'ed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@883 348d0f76-0448-11de-a6fe-93d51630548a
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aaron
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package org.broadinstitute.sting.playground.gatk.walkers;
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import net.sf.samtools.SAMRecord;
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import java.text.DecimalFormat;
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import java.text.NumberFormat;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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/*
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* Copyright (c) 2009 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* @author aaron
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* <p/>
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* Class FlagStatReadWalker
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* <p/>
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* This walker mirrors that stats that are generated by the flagstat
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* command of samtools.
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*/
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public class FlagStatReadWalker extends ReadWalker<Integer, Integer> {
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// what comes out of the flagstat
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class FlagStat {
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int readCount = 0;
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int QC_failure = 0;
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int duplicates = 0;
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int mapped = 0;
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int paired_in_sequencing = 0;
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int read1 = 0;
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int read2 = 0;
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int properly_paired = 0;
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int with_itself_and_mate_mapped = 0;
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int singletons = 0;
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int with_mate_mapped_to_a_different_chr = 0;
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int with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5 = 0;
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public String toString() {
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String ret = "";
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StringBuilder builder = new StringBuilder(ret);
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NumberFormat percentFormatter = new DecimalFormat("#0.00");
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builder.append(readCount);
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builder.append(" in total\n");
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builder.append(QC_failure);
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builder.append(" QC failure\n");
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builder.append(duplicates);
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builder.append(" duplicates\n");
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builder.append(mapped);
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builder.append(" mapped (");
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builder.append(percentFormatter.format(( (float)mapped / (float)readCount ) * 100.0));
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builder.append("%)\n");
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builder.append(paired_in_sequencing);
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builder.append(" paired in sequencing\n");
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builder.append(read1);
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builder.append(" read1\n");
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builder.append(read2);
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builder.append(" read2\n");
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builder.append(properly_paired);
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builder.append(" properly paired (");
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builder.append(percentFormatter.format(( (float)properly_paired / (float)readCount ) * 100.0));
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builder.append("%)\n");
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builder.append(with_itself_and_mate_mapped);
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builder.append(" with itself and mate mapped\n");
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builder.append(singletons);
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builder.append(" singletons (");
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builder.append(percentFormatter.format(( (float)singletons / (float)readCount ) * 100.0));
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builder.append("%)\n");
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builder.append(with_mate_mapped_to_a_different_chr);
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builder.append(" with mate mapped to a different chr\n");
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builder.append(with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5);
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builder.append(" with mate mapped to a different chr (mapQ>=5)");
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return builder.toString();
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}
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}
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private FlagStat myStat = new FlagStat();
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public Integer map( char[] ref, SAMRecord read ) {
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myStat.readCount++;
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if (read.getReadFailsVendorQualityCheckFlag()) {
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myStat.QC_failure++;
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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.getReferenceIndex() >= 0) {
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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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}
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if (read.getProperPairFlag()) {
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myStat.properly_paired++;
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}
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if (!read.getMateUnmappedFlag() && read.getReferenceIndex() >= 0) {
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myStat.with_itself_and_mate_mapped++;
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}
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if (read.getMateUnmappedFlag()) {
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myStat.singletons++;
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}
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}
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if (read.getReferenceIndex() >= 0 && read.getMateReferenceIndex() >= 0 && read.getReferenceIndex() != read.getMateReferenceIndex()) {
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myStat.with_mate_mapped_to_a_different_chr++;
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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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}
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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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() {
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return 0;
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}
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public Integer reduce
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( Integer
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value, Integer
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sum ) {
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return value + sum;
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}
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public void onTraversalDone
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( Integer
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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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}
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}
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