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update the documentation for CombineDuplicates for the new help system. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2324 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-12-11 17:01:42 +00:00
parent 420725441a
commit 86dc98bfb5
2 changed files with 17 additions and 31 deletions
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8
java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
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@ -46,14 +46,6 @@ import java.util.Arrays;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
/**
*
* User: aaron
* Date: Apr 24, 2009
* Time: 10:35:22 AM
*/
/** /**
* @author Mark DePristo * @author Mark DePristo
* @version 0.1 * @version 0.1

40
java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CombineDuplicatesWalker.java
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@ -12,11 +12,8 @@ import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMFileWriter;
/** /**
* Created by IntelliJ IDEA. * Process the input bam file, optionally emitting all the unique reads found, and emitting the combined duplicate reads to
* User: mdepristo * the specified output BAM location. If no output location is specified, the reads are written to STDOUT.
* Date: Feb 22, 2009
* Time: 2:52:28 PM
* To change this template use File | Settings | File Templates.
*/ */
public class CombineDuplicatesWalker extends DuplicateWalker<SAMRecord, SAMFileWriter> { public class CombineDuplicatesWalker extends DuplicateWalker<SAMRecord, SAMFileWriter> {
@Argument(fullName="outputBAM", shortName="outputBAM", required=false, doc="BAM File to write combined duplicates to") @Argument(fullName="outputBAM", shortName="outputBAM", required=false, doc="BAM File to write combined duplicates to")
@ -29,28 +26,24 @@ public class CombineDuplicatesWalker extends DuplicateWalker<SAMRecord, SAMFileW
doc="The maximum Q score allowed for combined reads, reflects the background error rate giving rise to perfect bases that don't correspond to the reference") doc="The maximum Q score allowed for combined reads, reflects the background error rate giving rise to perfect bases that don't correspond to the reference")
public int MAX_QUALITY_SCORE = 50; public int MAX_QUALITY_SCORE = 50;
final boolean DEBUG = false; /**
* do we want to include unqiue reads?
* @return the user specified command line argument INCLUDE_UNIQUE_READS
*/
public boolean mapUniqueReadsTooP() { public boolean mapUniqueReadsTooP() {
return INCLUDE_UNIQUE_READS; return INCLUDE_UNIQUE_READS;
} }
// ----------------------------------------------------------------------------------------------- /**
// Standard i/o reduce * start the walker with the command line argument specified SAMFileWriter
// * @return a sam file writer, which may be null
public void onTraversalDone(SAMFileWriter output) { */
if ( output != null ) {
output.close();
}
}
public SAMFileWriter reduceInit() { public SAMFileWriter reduceInit() {
return outputBAM; return outputBAM;
} }
/** /**
* * emit the read that was produced by combining the dupplicates
*
*/ */
public SAMFileWriter reduce(SAMRecord read, SAMFileWriter output) { public SAMFileWriter reduce(SAMRecord read, SAMFileWriter output) {
if ( output != null ) { if ( output != null ) {
@ -67,11 +60,12 @@ public class CombineDuplicatesWalker extends DuplicateWalker<SAMRecord, SAMFileW
* set, it's considered unique and returned. If there's more than one, the N-way combine * set, it's considered unique and returned. If there's more than one, the N-way combine
* duplicate function is invoked. * duplicate function is invoked.
* *
* @param loc * @param loc the genome loc
* @param refBases * @param refBases the reference bases for the given locus
* @param context * @param context the alignment context that has the reads information
* @param duplicateReads * @param duplicateReads a list of the dupplicate reads at this locus
* @return * @param uniqueReads the unique read list at this locus
* @return a read that combines the dupplicate reads at this locus
*/ */
public SAMRecord map(GenomeLoc loc, byte[] refBases, AlignmentContext context, public SAMRecord map(GenomeLoc loc, byte[] refBases, AlignmentContext context,
List<SAMRecord> uniqueReads, List<SAMRecord> uniqueReads,