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new default syntax 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@627 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-05-07 18:16:53 +00:00
parent 283a4d1b54
commit 4a26f35caa
2 changed files with 8 additions and 8 deletions
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12
java/src/org/broadinstitute/sting/playground/gatk/walkers/CombineDuplicatesWalker.java
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@ -27,15 +27,15 @@ import net.sf.samtools.SAMFileHeader;
* To change this template use File | Settings | File Templates.
*/
public class CombineDuplicatesWalker extends DuplicateWalker<SAMRecord, SAMFileWriter> {
@Argument(fullName="outputBAM", shortName="outputBAM", required=false, defaultValue="", doc="BAM File to write combined duplicates to")
public String outputFilename;
@Argument(fullName="outputBAM", shortName="outputBAM", required=false, doc="BAM File to write combined duplicates to")
public String outputFilename = null;
@Argument(fullName="includeUniqueReads", shortName="includeUniqueReads", required=false, defaultValue="true", doc="If true, also writes out non-duplicate reads in file")
public boolean INCLUDE_UNIQUE_READS;
@Argument(fullName="includeUniqueReads", shortName="includeUniqueReads", required=false, doc="If true, also writes out non-duplicate reads in file")
public boolean INCLUDE_UNIQUE_READS = true;
@Argument(fullName="maxQ", shortName="maxQ", required=false, defaultValue="50",
@Argument(fullName="maxQ", shortName="maxQ", required=false,
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;
public int MAX_QUALITY_SCORE = 50;
final boolean DEBUG = false;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/DuplicateQualsWalker.java
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@ -100,8 +100,8 @@ public class DuplicateQualsWalker extends DuplicateWalker<List<DuplicateComp>, Q
@Argument(fullName="combinedQuals", shortName="combinedQuals", required=false, doc="Combine and assess pairwise base qualities")
public boolean COMBINE_QUALS = false;
@Argument(fullName="combineAllDups", shortName="combineAllDups", required=false, defaultValue="false", doc="Combine and assess pairwise base qualities")
public boolean COMBINE_ALL_DUPS;
@Argument(fullName="combineAllDups", shortName="combineAllDups", required=false, doc="Combine and assess pairwise base qualities")
public boolean COMBINE_ALL_DUPS = false;
final boolean DEBUG = false;
final private boolean ACTUALLY_DO_WORK = true;