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

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
View File

@ -46,14 +46,6 @@ import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
/**
*
* User: aaron
* Date: Apr 24, 2009
* Time: 10:35:22 AM
*/
/**
* @author Mark DePristo
* @version 0.1

40
java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CombineDuplicatesWalker.java
View File

@ -12,11 +12,8 @@ import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileWriter;
/**
* Created by IntelliJ IDEA.
* User: mdepristo
* Date: Feb 22, 2009
* Time: 2:52:28 PM
* To change this template use File | Settings | File Templates.
* Process the input bam file, optionally emitting all the unique reads found, and emitting the combined duplicate reads to
* the specified output BAM location. If no output location is specified, the reads are written to STDOUT.
*/
public class CombineDuplicatesWalker extends DuplicateWalker<SAMRecord, SAMFileWriter> {
@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")
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() {
return INCLUDE_UNIQUE_READS;
}
// -----------------------------------------------------------------------------------------------
// Standard i/o reduce
//
public void onTraversalDone(SAMFileWriter output) {
if ( output != null ) {
output.close();
}
}
/**
* start the walker with the command line argument specified SAMFileWriter
* @return a sam file writer, which may be null
*/
public SAMFileWriter reduceInit() {
return outputBAM;
}
/**
*
*
* emit the read that was produced by combining the dupplicates
*/
public SAMFileWriter reduce(SAMRecord read, SAMFileWriter output) {
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
* duplicate function is invoked.
*
* @param loc
* @param refBases
* @param context
* @param duplicateReads
* @return
* @param loc the genome loc
* @param refBases the reference bases for the given locus
* @param context the alignment context that has the reads information
* @param duplicateReads a list of the dupplicate reads at this locus
* @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,
List<SAMRecord> uniqueReads,