From d7d0b270d113c65132c32e491bb0764a60e76519 Mon Sep 17 00:00:00 2001 From: asivache Date: Tue, 22 Sep 2009 16:46:57 +0000 Subject: [PATCH] now supports blacklisting lanes (with -BL option will ignore reads from any of the specified lanes) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1682 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/indels/IndelGenotyperWalker.java | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java index fc5b4973a..81965dd6b 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java @@ -7,6 +7,8 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadFilters; import org.broadinstitute.sting.gatk.filters.Platform454Filter; import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter; +import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter; +import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper; import org.broadinstitute.sting.playground.utils.CircularArray; import org.broadinstitute.sting.utils.GenomeLoc; @@ -23,7 +25,7 @@ import java.util.List; import java.util.Set; -@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class}) +@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, PlatformUnitFilter.class}) public class IndelGenotyperWalker extends ReadWalker { @Argument(fullName="outputFile", shortName="O", doc="output file name (defaults to BED format)", required=true) java.io.File bed_file; @@ -56,7 +58,11 @@ public class IndelGenotyperWalker extends ReadWalker { @Argument(fullName="refseq", shortName="refseq", doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated as GENOMIC/UTR/INTRON/CODING", required=false) String RefseqFileName = null; - @Argument(fullName="indel_debug", shortName="idebug", doc="Detailed printout for debugging",required=false) Boolean DEBUG = false; + @Argument(fullName="blacklistedLanes", shortName="BL", + doc="Name of lanes (platform units) that should be ignored. Reads coming from these lanes will never be seen "+ + "by this application, so they will not contribute indels to consider and will not be counted.", required=false) + PlatformUnitFilterHelper dummy; + @Argument(fullName="indel_debug", shortName="idebug", doc="Detailed printout for debugging",required=false) Boolean DEBUG = false; private static int WINDOW_SIZE = 200; private RunningCoverage coverage;