Mercurial > repos > halley > gatk_2_7
view GenomeAnalysisTK-2.7-2-g6bda569/resources/CountLoci.java @ 0:1485d70afa12 draft default tip
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author | halley |
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date | Tue, 15 Oct 2013 03:09:34 -0400 |
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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.qc; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.NanoSchedulable; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; import java.io.PrintStream; /** * Walks over the input data set, calculating the total number of covered loci for diagnostic purposes. * * <p> * This is the simplest example of a locus walker. * </p> * * <h3>Input</h3> * <p> * One or more BAM files. * </p> * * <h3>Output</h3> * <p> * Number of loci traversed. If an output file name is provided, then the result will be written to that file. * Otherwise it will be sent to standard console output. * </p> * * <h3>Examples</h3> * <pre> * java -Xmx2g -jar GenomeAnalysisTK.jar \ * -T CountLoci \ * -R ref.fasta \ * -I input.bam \ * -o output.txt \ * [-L input.intervals] * </pre> * */ @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} ) public class CountLoci extends LocusWalker<Integer, Long> implements TreeReducible<Long>, NanoSchedulable { @Output PrintStream out; public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 1; } public Long reduceInit() { return 0l; } public Long reduce(Integer value, Long sum) { return value + sum; } /** * Reduces two subtrees together. In this case, the implementation of the tree reduce * is exactly the same as the implementation of the single reduce. */ public Long treeReduce(Long lhs, Long rhs) { return lhs + rhs; } public void onTraversalDone( Long c ) { out.println(c); } }