Merge pull request #305 from broadinstitute/dr_move_DownsampleReadsQC_to_private
Move DownsampleReadsQC walker to private
This commit is contained in:
Mark DePristo
commit
28d4c3debc
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/*
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* Copyright (c) 2012 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.readutils;
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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.downsampling.DownsamplingUtils;
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import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.DataSource;
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import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.LinkedList;
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/**
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*/
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@Requires({DataSource.READS, DataSource.REFERENCE})
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public class DownsampleReadsQC extends ReadWalker<GATKSAMRecord, Collection<GATKSAMRecord>> implements NanoSchedulable {
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@Output(doc="Write output to this BAM filename instead of STDOUT", required = true)
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StingSAMFileWriter out;
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@Argument(fullName = "minReadsPerAlignmentStart", shortName = "minReadsPerAlignmentStart", doc ="", required = false)
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private int minReadsPerAlignmentStart = 5;
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@Argument(fullName = "downsampleTo", shortName = "downsampleTo", doc ="", required = false)
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private int downsampleTo = 1000;
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/**
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* The initialize function.
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*/
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public void initialize() {
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// final boolean preSorted = true;
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// if (getToolkit() != null && getToolkit().getArguments().BQSR_RECAL_FILE != null && !NO_PG_TAG ) {
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// Utils.setupWriter(out, getToolkit(), getToolkit().getSAMFileHeader(), !preSorted, keep_records, this, PROGRAM_RECORD_NAME);
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// }
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}
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/**
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* The reads map function.
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*
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* @param ref the reference bases that correspond to our read, if a reference was provided
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* @param readIn the read itself, as a GATKSAMRecord
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* @return the read itself
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*/
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public GATKSAMRecord map( ReferenceContext ref, GATKSAMRecord readIn, RefMetaDataTracker metaDataTracker ) {
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return readIn;
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}
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/**
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* reduceInit is called once before any calls to the map function. We use it here to setup the output
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* bam file, if it was specified on the command line
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*
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* @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise
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*/
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public Collection<GATKSAMRecord> reduceInit() {
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return new LinkedList<GATKSAMRecord>();
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}
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/**
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* given a read and a output location, reduce by emitting the read
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*
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* @param read the read itself
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* @param output the output source
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* @return the SAMFileWriter, so that the next reduce can emit to the same source
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*/
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public Collection<GATKSAMRecord> reduce( GATKSAMRecord read, Collection<GATKSAMRecord> output ) {
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output.add(read);
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return output;
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}
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@Override
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public void onTraversalDone(Collection<GATKSAMRecord> result) {
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for ( final GATKSAMRecord read : DownsamplingUtils.levelCoverageByPosition(new ArrayList<GATKSAMRecord>(result), downsampleTo, minReadsPerAlignmentStart) )
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out.addAlignment(read);
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}
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}
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