zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

remove FixBAMSortOrder walker. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3830 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-07-19 17:27:23 +00:00
parent 35ce367898
commit 18b0114e25
1 changed files with 0 additions and 87 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

87
java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java
View File

@ -1,87 +0,0 @@
/*
* 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.gatk.walkers;
/* Motivation: BAM files created by samtools which are sorted often don't
* have the sort order set to 'coordinate' in the BAM header (instead it's
* marked as 'unsorted'. Because BAMs are binary files, there's no way to
* easily change the tag.
*
* This walker rewrites a BAM file so that the output is identical to the input
* except that the sort order tag is set to 'coordinate'.
*
* Important note: to run properly in the GATK, the '-U' flag must be used so that
* the input BAM file not be rejected by the system.
*/
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.commandline.Argument;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriterFactory;
import java.io.File;
/**
* Fixes slightly corrupted BAM files by rewriting the input BAM file, altering
* the header by changing the sort order tag (SO) to coordinate sort order. Will NOT
* verify the contents of the file to ensure that the data is actually in coordinate sorted
* order.
*/
public class FixBAMSortOrderTag extends ReadWalker<SAMRecord, SAMFileWriter> {
@Argument(required=true, shortName="out_bam", doc="The samfile to output to")
public File SAM_FILE_OUTPUT_LOCATION;
@Argument(required=false, shortName="sortorder", doc="the sort order to emit in")
public SAMFileHeader.SortOrder SORT_ORDER=SAMFileHeader.SortOrder.coordinate;
@Override
public SAMRecord map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
return read;
}
@Override
public SAMFileWriter reduceInit() {
SAMFileHeader header = GenomeAnalysisEngine.instance.getSAMFileHeader();
header.setSortOrder(SORT_ORDER);
SAMFileWriterFactory factory = new SAMFileWriterFactory();
return factory.makeBAMWriter(header,false,SAM_FILE_OUTPUT_LOCATION);
}
@Override
public SAMFileWriter reduce(SAMRecord value, SAMFileWriter sum) {
sum.addAlignment(value);
return sum;
}
public void onTraversalDone(SAMFileWriter result) {
result.close();
}
}