No one claimed this walker and it doesn't have integration tests or GATKdocs so it doesn't belong in public.
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Eric Banks
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/*
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* Copyright (c) 2010 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
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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.coverage;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import java.io.PrintStream;
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/**
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* Computes the coverage per every <granularity> bases on the reference, or on the subset of the reference
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* specified by the intervals provided. Moving to the next contig on the reference will always restart the
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* count anew, even if the count of bases in the last chunk on the previous contig did not reach specified <granularity>.
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*/
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public class CoarseCoverageWalker extends ReadWalker<Integer,Integer> {
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@Output
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public PrintStream out;
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@Argument(fullName="granularity", shortName="G", doc="Granularity", required=true)
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public Integer N;
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@Argument(fullName="dontZeroMissingContigs", shortName="Z", doc="If provided, we won't emit 0 counts for all sites on contigs skipped", required=true)
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public boolean dontZeroMissingContigs;
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private int chunkStart = 1; // start of the current chunk we are counting reads for
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private int contig = 0; // current contig we are on
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private int count = 0; // number of reads overlapping with the current chunk
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private static String zeroString = "0";
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@Override
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public void initialize() {
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chunkStart = 1;
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contig = 0;
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count = 0;
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}
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@Override
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public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
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if ( read.getReadUnmappedFlag() ||
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read.getDuplicateReadFlag() ||
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read.getNotPrimaryAlignmentFlag() ||
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read.getMappingQuality() == 0 ) return 0;
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if ( read.getReferenceIndex() != contig ) {
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// we jumped onto another contig
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out.printf("%d%n", count); // print old count
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count = 0;
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// if we skipped one or more contigs completely, make sure we print 0 counts over all of them:
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for ( contig++ ; contig < read.getReferenceIndex() ; contig++) {
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if ( ! dontZeroMissingContigs ) {
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int contigSize = read.getHeader().getSequence(contig).getSequenceLength();
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for ( int k = 1 ; k < contigSize ; k+=N ) out.println(zeroString);
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}
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}
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// by now we scrolled to the right contig
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chunkStart = 1; // reset chunk start
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}
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// if our read is past the boundary of the current chunk, print old count(s)
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// (for the current chunk and all chunks we may have skipped altogether) and reinitialize:
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while ( chunkStart+N < read.getAlignmentStart() ) {
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out.printf("%d%n", count); // print old count
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count = 0;
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chunkStart += N;
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}
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count++;
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return 1;
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}
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@Override
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public Integer reduce(Integer value, Integer sum) {
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return value+sum;
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}
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@Override
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public Integer reduceInit() {
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return 0;
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}
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@Override
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public void onTraversalDone(Integer result) {
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out.printf("%d%n", count); // print count from the last chunk
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super.onTraversalDone(result);
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}
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}
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