Retiring the alignment walkers and related integration test since we don't want to support them anymore.
This commit is contained in:
Eric Banks
parent
0f4acaae1b
commit
67d348a31d
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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.alignment;
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import net.sf.picard.reference.ReferenceSequenceFileFactory;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMSequenceDictionary;
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import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
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import org.broadinstitute.sting.alignment.bwa.BWTFiles;
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import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
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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.CommandLineGATK;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
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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 org.broadinstitute.sting.gatk.walkers.WalkerName;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import java.io.File;
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/**
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* Aligns reads to a given reference using Heng Li's BWA aligner, presenting the resulting alignments in SAM or BAM format.
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* Mimics the steps 'bwa aln' followed by 'bwa samse' using the BWA/C implementation.
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*
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* @author mhanna
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* @version 0.1
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*/
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@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
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@WalkerName("Align")
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public class AlignmentWalker extends ReadWalker<Integer,Integer> {
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@Argument(fullName="target_reference",shortName="target_ref",doc="The reference to which reads in the source file should be aligned. Alongside this reference should sit index files " +
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"generated by bwa index -d bwtsw. If unspecified, will default " +
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"to the reference specified via the -R argument.",required=false)
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private File targetReferenceFile = null;
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@Output
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private StingSAMFileWriter out = null;
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/**
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* The actual aligner.
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*/
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private BWACAligner aligner = null;
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/**
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* New header to use, if desired.
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*/
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private SAMFileHeader header;
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/**
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* Create an aligner object. The aligner object will load and hold the BWT until close() is called.
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*/
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@Override
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public void initialize() {
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if(targetReferenceFile == null)
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targetReferenceFile = getToolkit().getArguments().referenceFile;
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BWTFiles bwtFiles = new BWTFiles(targetReferenceFile.getAbsolutePath());
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BWAConfiguration configuration = new BWAConfiguration();
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aligner = new BWACAligner(bwtFiles,configuration);
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// Take the header of the SAM file, tweak it by adding in the reference dictionary and specifying that the target file is unsorted.
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header = getToolkit().getSAMFileHeader().clone();
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SAMSequenceDictionary referenceDictionary =
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ReferenceSequenceFileFactory.getReferenceSequenceFile(targetReferenceFile).getSequenceDictionary();
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header.setSequenceDictionary(referenceDictionary);
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header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
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out.writeHeader(header);
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}
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/**
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* Aligns a read to the given reference.
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*
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* @param ref Reference over the read. Read will most likely be unmapped, so ref will be null.
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* @param read Read to align.
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* @return Number of alignments found for this read.
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*/
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@Override
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public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
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SAMRecord alignedRead = aligner.align(read,header);
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out.addAlignment(alignedRead);
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return 1;
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}
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/**
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* Initial value for reduce. In this case, alignments will be counted.
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* @return 0, indicating no alignments yet found.
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*/
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@Override
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public Integer reduceInit() { return 0; }
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/**
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* Calculates the number of alignments found.
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* @param value Number of alignments found by this map.
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* @param sum Number of alignments found before this map.
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* @return Number of alignments found up to and including this map.
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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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/**
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* Cleanup.
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* @param result Number of reads processed.
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*/
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@Override
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public void onTraversalDone(Integer result) {
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aligner.close();
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super.onTraversalDone(result);
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}
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}
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@ -1,132 +0,0 @@
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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.alignment;
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import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
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import org.broadinstitute.sting.alignment.bwa.BWTFiles;
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import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
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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.CommandLineGATK;
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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 org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import java.io.PrintStream;
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import java.util.Iterator;
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import java.util.Map;
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import java.util.SortedMap;
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import java.util.TreeMap;
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/**
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* Counts the number of best alignments as presented by BWA and outputs a histogram of number of placements vs. the
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* frequency of that number of placements.
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*
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* @author mhanna
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* @version 0.1
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*/
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@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
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public class CountBestAlignments extends ReadWalker<Integer,Integer> {
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/**
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* The supporting BWT index generated using BWT.
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*/
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@Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
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private String prefix = null;
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@Output
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private PrintStream out = null;
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/**
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* The actual aligner.
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*/
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private Aligner aligner = null;
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private SortedMap<Integer,Integer> alignmentFrequencies = new TreeMap<Integer,Integer>();
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/**
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* Create an aligner object. The aligner object will load and hold the BWT until close() is called.
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*/
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@Override
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public void initialize() {
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if(prefix == null)
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prefix = getToolkit().getArguments().referenceFile.getAbsolutePath();
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BWTFiles bwtFiles = new BWTFiles(prefix);
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BWAConfiguration configuration = new BWAConfiguration();
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aligner = new BWACAligner(bwtFiles,configuration);
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}
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/**
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* Aligns a read to the given reference.
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*
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* @param ref Reference over the read. Read will most likely be unmapped, so ref will be null.
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* @param read Read to align.
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* @return Number of alignments found for this read.
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*/
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@Override
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public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
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Iterator<Alignment[]> alignmentIterator = aligner.getAllAlignments(read.getReadBases()).iterator();
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if(alignmentIterator.hasNext()) {
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int numAlignments = alignmentIterator.next().length;
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if(alignmentFrequencies.containsKey(numAlignments))
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alignmentFrequencies.put(numAlignments,alignmentFrequencies.get(numAlignments)+1);
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else
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alignmentFrequencies.put(numAlignments,1);
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}
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return 1;
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}
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/**
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* Initial value for reduce. In this case, validated reads will be counted.
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* @return 0, indicating no reads yet validated.
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*/
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@Override
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public Integer reduceInit() { return 0; }
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/**
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* Calculates the number of reads processed.
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* @param value Number of reads processed by this map.
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* @param sum Number of reads processed before this map.
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* @return Number of reads processed up to and including this map.
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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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/**
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* Cleanup.
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* @param result Number of reads processed.
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*/
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@Override
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public void onTraversalDone(Integer result) {
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aligner.close();
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for(Map.Entry<Integer,Integer> alignmentFrequency: alignmentFrequencies.entrySet())
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out.printf("%d\t%d%n", alignmentFrequency.getKey(), alignmentFrequency.getValue());
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super.onTraversalDone(result);
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}
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}
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package org.broadinstitute.sting.alignment;
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import org.testng.annotations.Test;
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import org.broadinstitute.sting.WalkerTest;
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import java.util.Arrays;
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/**
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* Integration tests for the aligner.
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*
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* @author mhanna
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* @version 0.1
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*/
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public class AlignerIntegrationTest extends WalkerTest {
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@Test
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public void testBasicAlignment() {
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String md5 = "a2bdf907b18114a86ca47f9fc23791bf";
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-R " + GATKDataLocation + "bwa/human_b36_both.fasta" +
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" -T Align" +
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" -I " + validationDataLocation + "NA12878_Pilot1_20.trimmed.unmapped.bam" +
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" -o %s",
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1, // just one output file
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Arrays.asList(md5));
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executeTest("testBasicAlignment", spec);
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}
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}
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