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Merge pull request #305 from broadinstitute/dr_move_DownsampleReadsQC_to_private 

Move DownsampleReadsQC walker to private
This commit is contained in:
Mark DePristo 2013-06-25 16:33:20 -07:00
parent d13ed06e9d 94294ed6c4
commit 28d4c3debc
1 changed files with 0 additions and 105 deletions
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105
public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/DownsampleReadsQC.java
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/*
* Copyright (c) 2012 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.readutils;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.downsampling.DownsamplingUtils;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedList;
/**
*/
@Requires({DataSource.READS, DataSource.REFERENCE})
public class DownsampleReadsQC extends ReadWalker<GATKSAMRecord, Collection<GATKSAMRecord>> implements NanoSchedulable {
@Output(doc="Write output to this BAM filename instead of STDOUT", required = true)
StingSAMFileWriter out;
@Argument(fullName = "minReadsPerAlignmentStart", shortName = "minReadsPerAlignmentStart", doc ="", required = false)
private int minReadsPerAlignmentStart = 5;
@Argument(fullName = "downsampleTo", shortName = "downsampleTo", doc ="", required = false)
private int downsampleTo = 1000;
/**
* The initialize function.
*/
public void initialize() {
// final boolean preSorted = true;
// if (getToolkit() != null && getToolkit().getArguments().BQSR_RECAL_FILE != null && !NO_PG_TAG ) {
// Utils.setupWriter(out, getToolkit(), getToolkit().getSAMFileHeader(), !preSorted, keep_records, this, PROGRAM_RECORD_NAME);
// }
}
/**
* The reads map function.
*
* @param ref the reference bases that correspond to our read, if a reference was provided
* @param readIn the read itself, as a GATKSAMRecord
* @return the read itself
*/
public GATKSAMRecord map( ReferenceContext ref, GATKSAMRecord readIn, RefMetaDataTracker metaDataTracker ) {
return readIn;
}
/**
* reduceInit is called once before any calls to the map function. We use it here to setup the output
* bam file, if it was specified on the command line
*
* @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise
*/
public Collection<GATKSAMRecord> reduceInit() {
return new LinkedList<GATKSAMRecord>();
}
/**
* given a read and a output location, reduce by emitting the read
*
* @param read the read itself
* @param output the output source
* @return the SAMFileWriter, so that the next reduce can emit to the same source
*/
public Collection<GATKSAMRecord> reduce( GATKSAMRecord read, Collection<GATKSAMRecord> output ) {
output.add(read);
return output;
}
@Override
public void onTraversalDone(Collection<GATKSAMRecord> result) {
for ( final GATKSAMRecord read : DownsamplingUtils.levelCoverageByPosition(new ArrayList<GATKSAMRecord>(result), downsampleTo, minReadsPerAlignmentStart) )
out.addAlignment(read);
}
}