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I want to be the first to use the new super-cool Hidden annotation! No more telling people not to use the cleaner debugging options. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3947 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-05 02:44:37 +00:00
parent 78bfe6ac48
commit f247cbf68e
1 changed files with 4 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.Hidden;
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
@ -112,12 +113,15 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// DEBUGGING OPTIONS FOLLOW
@Hidden
@Argument(fullName="indelsFileForDebugging", shortName="indels", required=false, doc="Output file (text) for the indels found; FOR DEBUGGING PURPOSES ONLY")
protected String OUT_INDELS = null;
@Hidden
@Argument(fullName="statisticsFileForDebugging", shortName="stats", doc="print out statistics (what does or doesn't get cleaned); FOR DEBUGGING PURPOSES ONLY", required=false)
protected String OUT_STATS = null;
@Hidden
@Argument(fullName="SNPsFileForDebugging", shortName="snps", doc="print out whether mismatching columns do or don't get cleaned out; FOR DEBUGGING PURPOSES ONLY", required=false)
protected String OUT_SNPS = null;