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Quick fix for Danny Lieber: flesh out the additional functionality required 

to align to a reference other than what's specified in the header.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5133 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-01-31 05:28:37 +00:00
parent b5d1aab8dc
commit 5e7a5cf924
3 changed files with 19 additions and 30 deletions
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6
java/src/org/broadinstitute/sting/alignment/Alignment.java
View File

@ -195,6 +195,12 @@ public class Alignment {
if(newSAMHeader != null)
read.setHeader(newSAMHeader);
// If we're realigning a previously aligned record, strip out the placement of the alignment.
read.setReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
read.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
read.setMateReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
read.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
if(alignment != null) {
read.setReadUmappedFlag(false);
read.setReferenceIndex(alignment.getContigIndex());

41
java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.sting.alignment;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
@ -49,28 +50,19 @@ import java.io.PrintStream;
*/
@WalkerName("Align")
public class AlignmentWalker extends ReadWalker<Integer,Integer> {
@Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
private String prefix = null;
@Argument(fullName = "outputBam", shortName = "ob", doc = "Write output to this BAM filename instead of STDOUT", required = false)
private String outputBamFile = null;
@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 PrintStream out = null;
@Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false)
private Integer bamCompression = 5;
private StingSAMFileWriter out = null;
/**
* The actual aligner.
*/
private BWACAligner aligner = null;
/**
* Target for reads to output.
*/
private SAMFileWriter outputBam = null;
/**
* New header to use, if desired.
*/
@ -81,23 +73,20 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
*/
@Override
public void initialize() {
if(prefix == null)
prefix = getToolkit().getArguments().referenceFile.getAbsolutePath();
BWTFiles bwtFiles = new BWTFiles(prefix);
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(getToolkit().getArguments().referenceFile).getSequenceDictionary();
ReferenceSequenceFileFactory.getReferenceSequenceFile(targetReferenceFile).getSequenceDictionary();
header.setSequenceDictionary(referenceDictionary);
header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
if (outputBamFile != null) {
SAMFileWriterFactory factory = new SAMFileWriterFactory();
outputBam = factory.makeBAMWriter(header, false, new File(outputBamFile), bamCompression);
}
out.writeHeader(header);
}
/**
@ -109,11 +98,7 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
@Override
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
SAMRecord alignedRead = aligner.align(read,header);
if (outputBam != null) {
outputBam.addAlignment(alignedRead);
} else {
out.println(alignedRead.format());
}
out.addAlignment(alignedRead);
return 1;
}
@ -142,8 +127,6 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
@Override
public void onTraversalDone(Integer result) {
aligner.close();
if (outputBam != null)
outputBam.close();
super.onTraversalDone(result);
}

2
java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java
View File

@ -19,7 +19,7 @@ public class AlignerIntegrationTest extends WalkerTest {
"-R /humgen/gsa-scr1/GATK_Data/bwa/human_b36_both.fasta" +
" -T Align" +
" -I " + validationDataLocation + "NA12878_Pilot1_20.trimmed.unmapped.bam" +
" -ob %s",
" -o %s",
1, // just one output file
Arrays.asList(md5));
executeTest("testBasicAlignment", spec);