From f247cbf68e0f4bd40bb890b006f47aa44f87f1a0 Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 5 Aug 2010 02:44:37 +0000 Subject: [PATCH] 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 --- .../sting/gatk/walkers/indels/IndelRealigner.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 4a814b1a0..bda9babf8 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -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 { // 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;