Merged bug fix from Stable into Unstable
This commit is contained in:
Matt Hanna
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/*
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* Copyright (c) 2010.
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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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.qc;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.walkers.ReadPairWalker;
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import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
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import java.io.PrintStream;
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import java.util.Collection;
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import java.util.List;
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/**
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* Counts the number of read pairs encountered in a file sorted in
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* query name order. Breaks counts down by total pairs and number
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* of paired reads.
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*
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*
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* <h2>Input</h2>
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* <p>
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* One or more bam files.
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* </p>
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*
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* <h2>Output</h2>
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* <p>
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* Number of pairs seen.
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* </p>
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*
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* <h2>Examples</h2>
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* <pre>
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* java -Xmx2g -jar GenomeAnalysisTK.jar \
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* -R ref.fasta \
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* -T CountPairs \
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* -o output.txt \
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* -I input.bam
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* </pre>
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*
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* @author mhanna
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*/
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public class CountPairsWalker extends ReadPairWalker<Integer,Long> {
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@Output
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private PrintStream out;
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/**
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* How many reads are the first in a pair, based on flag 0x0040 from the SAM spec.
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*/
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private long firstOfPair = 0;
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/**
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* How many reads are the second in a pair, based on flag 0x0080 from the SAM spec.
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*/
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private long secondOfPair = 0;
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/**
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* A breakdown of the total number of reads seen with exactly the same read name.
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*/
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private List<Long> pairCountsByType = new ExpandingArrayList<Long>();
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/**
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* Maps a read pair to a given reduce of type MapType. Semantics determined by subclasser.
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* @param reads Collection of reads having the same name.
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* @return Semantics defined by implementer.
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*/
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@Override
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public Integer map(Collection<SAMRecord> reads) {
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if(pairCountsByType.get(reads.size()) != null)
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pairCountsByType.set(reads.size(),pairCountsByType.get(reads.size())+1);
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else
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pairCountsByType.set(reads.size(),1L);
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for(SAMRecord read: reads) {
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if(read.getFirstOfPairFlag()) firstOfPair++;
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if(read.getSecondOfPairFlag()) secondOfPair++;
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}
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return 1;
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}
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/**
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* No pairs at the beginning of a traversal.
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* @return 0 always.
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*/
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@Override
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public Long reduceInit() {
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return 0L;
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}
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/**
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* Combine number of pairs seen in this iteration (always 1) with total number of pairs
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* seen in previous iterations.
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* @param value Pairs in this iteration (1), from the map function.
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* @param sum Count of all pairs in prior iterations.
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* @return All pairs encountered in previous iterations + all pairs encountered in this iteration (sum + 1).
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*/
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@Override
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public Long reduce(Integer value, Long sum) {
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return value + sum;
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}
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/**
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* Print summary statistics over the entire traversal.
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* @param sum A count of all read pairs viewed.
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*/
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@Override
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public void onTraversalDone(Long sum) {
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out.printf("Total number of pairs : %d%n",sum);
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out.printf("Total number of first reads in pair : %d%n",firstOfPair);
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out.printf("Total number of second reads in pair: %d%n",secondOfPair);
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for(int i = 1; i < pairCountsByType.size(); i++) {
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if(pairCountsByType.get(i) == null)
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continue;
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out.printf("Pairs of size %d: %d%n",i,pairCountsByType.get(i));
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}
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}
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}
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