Adding documentation before the release for GATK wiki page
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@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
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* @version 0.1
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*/
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public class PlatformFilter extends ReadFilter {
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@Argument(fullName = "PLFilterName", shortName = "PLFilterName", doc="Discard reads with RG:PL attribute containing this strign", required=false)
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@Argument(fullName = "PLFilterName", shortName = "PLFilterName", doc="Discard reads with RG:PL attribute containing this string", required=false)
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protected String[] PLFilterNames;
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public boolean filterOut(SAMRecord rec) {
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@ -68,6 +68,13 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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* -I input1.bam \
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* -I input2.bam \
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* --read_filter MappingQualityZero
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*
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* java -Xmx2g -jar GenomeAnalysisTK.jar \
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* -R ref.fasta \
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* -T PrintReads \
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* -o output.bam \
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* -I input.bam \
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* -n 2000
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* </pre>
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*
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*/
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