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For dealing with slightly malformatted BAMs - mark every alignment as primary, or in the case of some BAM files from UWash, supply the sample information for each read group. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3340 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-05-10 15:17:05 +00:00
parent 4a7902bb8e
commit 13fd182b7c
2 changed files with 83 additions and 0 deletions
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39
java/src/org/broadinstitute/sting/oneoffprojects/tools/MarkAllAlignmentsAsPrimary.java 100755
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package org.broadinstitute.sting.oneoffprojects.tools;
import net.sf.picard.cmdline.CommandLineProgram;
import net.sf.picard.cmdline.Usage;
import net.sf.picard.cmdline.Option;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileWriterFactory;
import java.io.*;
public class MarkAllAlignmentsAsPrimary extends CommandLineProgram {
@Usage(programVersion="1.0") public String USAGE = "Mark all alignments as primary.";
@Option(shortName="I", doc="Input file (bam or sam) to extract reads from. If not specified, reads from stdin.",
optional=true) public File IN = null;
@Option(shortName="O",doc="Output file (bam or sam).",
optional=true) public File OUT = null;
public static void main(final String[] argv) {
System.exit(new MarkAllAlignmentsAsPrimary().instanceMain(argv));
}
protected int doWork() {
SAMFileReader inReader = new SAMFileReader(IN);
SAMFileWriter outWriter = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(inReader.getFileHeader(), true, OUT);
for (SAMRecord read : inReader ) {
read.setNotPrimaryAlignmentFlag(false);
outWriter.addAlignment(read);
}
inReader.close();
outWriter.close();
return 0;
}
}

44
java/src/org/broadinstitute/sting/oneoffprojects/tools/RepairSeattleBAM.java 100755
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package org.broadinstitute.sting.oneoffprojects.tools;
import net.sf.picard.cmdline.CommandLineProgram;
import net.sf.picard.cmdline.Usage;
import net.sf.picard.cmdline.Option;
import net.sf.samtools.*;
import java.io.*;
public class RepairSeattleBAM extends CommandLineProgram {
@Usage(programVersion="1.0") public String USAGE = "Fix read group info";
@Option(shortName="I", doc="Input file (bam or sam) to extract reads from. If not specified, reads from stdin.",
optional=true) public File IN = null;
@Option(shortName="O",doc="Output file (bam or sam).",
optional=true) public File OUT = null;
@Option(shortName="S",doc="Sample.",
optional=true) public String SAMPLE = null;
public static void main(final String[] argv) {
System.exit(new RepairSeattleBAM().instanceMain(argv));
}
protected int doWork() {
SAMFileReader inReader = new SAMFileReader(IN);
for (SAMReadGroupRecord rg : inReader.getFileHeader().getReadGroups()) {
rg.setSample(SAMPLE);
}
SAMFileWriter outWriter = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(inReader.getFileHeader(), true, OUT);
for (SAMRecord read : inReader ) {
//read.getReadGroup().setSample(SAMPLE);
read.setAttribute("SM", SAMPLE);
outWriter.addAlignment(read);
}
inReader.close();
outWriter.close();
return 0;
}
}