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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
This commit is contained in:
asivache 2009-09-22 16:46:57 +00:00
parent 57d31b8e9b
commit d7d0b270d1
1 changed files with 8 additions and 2 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -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<Integer,Integer> {
@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<Integer,Integer> {
@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;