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Retiring the alignment walkers and related integration test since we don't want to support them anymore.

This commit is contained in:
Eric Banks 2012-08-28 10:16:49 -04:00
parent 0f4acaae1b
commit 67d348a31d
3 changed files with 0 additions and 298 deletions
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139
public/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.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.alignment;
import net.sf.picard.reference.ReferenceSequenceFileFactory;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.BWTFiles;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.File;
/**
* Aligns reads to a given reference using Heng Li's BWA aligner, presenting the resulting alignments in SAM or BAM format.
* Mimics the steps 'bwa aln' followed by 'bwa samse' using the BWA/C implementation.
*
* @author mhanna
* @version 0.1
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@WalkerName("Align")
public class AlignmentWalker extends ReadWalker<Integer,Integer> {
@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 " +
"generated by bwa index -d bwtsw. If unspecified, will default " +
"to the reference specified via the -R argument.",required=false)
private File targetReferenceFile = null;
@Output
private StingSAMFileWriter out = null;
/**
* The actual aligner.
*/
private BWACAligner aligner = null;
/**
* New header to use, if desired.
*/
private SAMFileHeader header;
/**
* Create an aligner object. The aligner object will load and hold the BWT until close() is called.
*/
@Override
public void initialize() {
if(targetReferenceFile == null)
targetReferenceFile = getToolkit().getArguments().referenceFile;
BWTFiles bwtFiles = new BWTFiles(targetReferenceFile.getAbsolutePath());
BWAConfiguration configuration = new BWAConfiguration();
aligner = new BWACAligner(bwtFiles,configuration);
// Take the header of the SAM file, tweak it by adding in the reference dictionary and specifying that the target file is unsorted.
header = getToolkit().getSAMFileHeader().clone();
SAMSequenceDictionary referenceDictionary =
ReferenceSequenceFileFactory.getReferenceSequenceFile(targetReferenceFile).getSequenceDictionary();
header.setSequenceDictionary(referenceDictionary);
header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
out.writeHeader(header);
}
/**
* Aligns a read to the given reference.
*
* @param ref Reference over the read. Read will most likely be unmapped, so ref will be null.
* @param read Read to align.
* @return Number of alignments found for this read.
*/
@Override
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
SAMRecord alignedRead = aligner.align(read,header);
out.addAlignment(alignedRead);
return 1;
}
/**
* Initial value for reduce. In this case, alignments will be counted.
* @return 0, indicating no alignments yet found.
*/
@Override
public Integer reduceInit() { return 0; }
/**
* Calculates the number of alignments found.
* @param value Number of alignments found by this map.
* @param sum Number of alignments found before this map.
* @return Number of alignments found up to and including this map.
*/
@Override
public Integer reduce(Integer value, Integer sum) {
return value + sum;
}
/**
* Cleanup.
* @param result Number of reads processed.
*/
@Override
public void onTraversalDone(Integer result) {
aligner.close();
super.onTraversalDone(result);
}
}

132
public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.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.alignment;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.BWTFiles;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.PrintStream;
import java.util.Iterator;
import java.util.Map;
import java.util.SortedMap;
import java.util.TreeMap;
/**
* Counts the number of best alignments as presented by BWA and outputs a histogram of number of placements vs. the
* frequency of that number of placements.
*
* @author mhanna
* @version 0.1
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
public class CountBestAlignments extends ReadWalker<Integer,Integer> {
/**
* The supporting BWT index generated using BWT.
*/
@Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
private String prefix = null;
@Output
private PrintStream out = null;
/**
* The actual aligner.
*/
private Aligner aligner = null;
private SortedMap<Integer,Integer> alignmentFrequencies = new TreeMap<Integer,Integer>();
/**
* Create an aligner object. The aligner object will load and hold the BWT until close() is called.
*/
@Override
public void initialize() {
if(prefix == null)
prefix = getToolkit().getArguments().referenceFile.getAbsolutePath();
BWTFiles bwtFiles = new BWTFiles(prefix);
BWAConfiguration configuration = new BWAConfiguration();
aligner = new BWACAligner(bwtFiles,configuration);
}
/**
* Aligns a read to the given reference.
*
* @param ref Reference over the read. Read will most likely be unmapped, so ref will be null.
* @param read Read to align.
* @return Number of alignments found for this read.
*/
@Override
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
Iterator<Alignment[]> alignmentIterator = aligner.getAllAlignments(read.getReadBases()).iterator();
if(alignmentIterator.hasNext()) {
int numAlignments = alignmentIterator.next().length;
if(alignmentFrequencies.containsKey(numAlignments))
alignmentFrequencies.put(numAlignments,alignmentFrequencies.get(numAlignments)+1);
else
alignmentFrequencies.put(numAlignments,1);
}
return 1;
}
/**
* Initial value for reduce. In this case, validated reads will be counted.
* @return 0, indicating no reads yet validated.
*/
@Override
public Integer reduceInit() { return 0; }
/**
* Calculates the number of reads processed.
* @param value Number of reads processed by this map.
* @param sum Number of reads processed before this map.
* @return Number of reads processed up to and including this map.
*/
@Override
public Integer reduce(Integer value, Integer sum) {
return value + sum;
}
/**
* Cleanup.
* @param result Number of reads processed.
*/
@Override
public void onTraversalDone(Integer result) {
aligner.close();
for(Map.Entry<Integer,Integer> alignmentFrequency: alignmentFrequencies.entrySet())
out.printf("%d\t%d%n", alignmentFrequency.getKey(), alignmentFrequency.getValue());
super.onTraversalDone(result);
}
}

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public/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java
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package org.broadinstitute.sting.alignment;
import org.testng.annotations.Test;
import org.broadinstitute.sting.WalkerTest;
import java.util.Arrays;
/**
* Integration tests for the aligner.
*
* @author mhanna
* @version 0.1
*/
public class AlignerIntegrationTest extends WalkerTest {
@Test
public void testBasicAlignment() {
String md5 = "a2bdf907b18114a86ca47f9fc23791bf";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + GATKDataLocation + "bwa/human_b36_both.fasta" +
" -T Align" +
" -I " + validationDataLocation + "NA12878_Pilot1_20.trimmed.unmapped.bam" +
" -o %s",
1, // just one output file
Arrays.asList(md5));
executeTest("testBasicAlignment", spec);
}
}