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No one claimed this walker and it doesn't have integration tests or GATKdocs so it doesn't belong in public.

This commit is contained in:
Eric Banks 2011-10-10 15:17:54 -04:00
parent fb72bcf732
commit 77c983c5b5
1 changed files with 0 additions and 118 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
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/*
* Copyright (c) 2010 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.coverage;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import java.io.PrintStream;
/**
* Computes the coverage per every <granularity> bases on the reference, or on the subset of the reference
* specified by the intervals provided. Moving to the next contig on the reference will always restart the
* count anew, even if the count of bases in the last chunk on the previous contig did not reach specified <granularity>.
*/
public class CoarseCoverageWalker extends ReadWalker<Integer,Integer> {
@Output
public PrintStream out;
@Argument(fullName="granularity", shortName="G", doc="Granularity", required=true)
public Integer N;
@Argument(fullName="dontZeroMissingContigs", shortName="Z", doc="If provided, we won't emit 0 counts for all sites on contigs skipped", required=true)
public boolean dontZeroMissingContigs;
private int chunkStart = 1; // start of the current chunk we are counting reads for
private int contig = 0; // current contig we are on
private int count = 0; // number of reads overlapping with the current chunk
private static String zeroString = "0";
@Override
public void initialize() {
chunkStart = 1;
contig = 0;
count = 0;
}
@Override
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
if ( read.getReadUnmappedFlag() ||
read.getDuplicateReadFlag() ||
read.getNotPrimaryAlignmentFlag() ||
read.getMappingQuality() == 0 ) return 0;
if ( read.getReferenceIndex() != contig ) {
// we jumped onto another contig
out.printf("%d%n", count); // print old count
count = 0;
// if we skipped one or more contigs completely, make sure we print 0 counts over all of them:
for ( contig++ ; contig < read.getReferenceIndex() ; contig++) {
if ( ! dontZeroMissingContigs ) {
int contigSize = read.getHeader().getSequence(contig).getSequenceLength();
for ( int k = 1 ; k < contigSize ; k+=N ) out.println(zeroString);
}
}
// by now we scrolled to the right contig
chunkStart = 1; // reset chunk start
}
// if our read is past the boundary of the current chunk, print old count(s)
// (for the current chunk and all chunks we may have skipped altogether) and reinitialize:
while ( chunkStart+N < read.getAlignmentStart() ) {
out.printf("%d%n", count); // print old count
count = 0;
chunkStart += N;
}
count++;
return 1;
}
@Override
public Integer reduce(Integer value, Integer sum) {
return value+sum;
}
@Override
public Integer reduceInit() {
return 0;
}
@Override
public void onTraversalDone(Integer result) {
out.printf("%d%n", count); // print count from the last chunk
super.onTraversalDone(result);
}
}