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use the filter to ignore 454 reads in the traversal to speed up cleaning 

(since there's less area to actually clean against)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1220 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-10 18:34:44 +00:00
parent 0070b8ea6a
commit dea72c576e
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -4,18 +4,20 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.LocusWindowWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.filters.Platform454Filter;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.playground.indels.*;
import net.sf.samtools.*;
import net.sf.samtools.SAMFileHeader.SortOrder;
import java.util.*;
import java.io.File;
import java.io.FileWriter;
@WalkerName("IntervalCleaner")
@ReadFilters(Platform454Filter.class)
public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer> {
@Argument(fullName="allow454Reads", shortName="454", doc="process 454 reads", required=false)
boolean allow454 = false;