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Adding documentation before the release for GATK wiki page

This commit is contained in:
Eric Banks 2011-09-15 13:56:23 -04:00
parent 202405b1a1
commit d369d10593
2 changed files with 8 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
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@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
* @version 0.1 * @version 0.1
*/ */
public class PlatformFilter extends ReadFilter { public class PlatformFilter extends ReadFilter {
@Argument(fullName = "PLFilterName", shortName = "PLFilterName", doc="Discard reads with RG:PL attribute containing this strign", required=false) @Argument(fullName = "PLFilterName", shortName = "PLFilterName", doc="Discard reads with RG:PL attribute containing this string", required=false)
protected String[] PLFilterNames; protected String[] PLFilterNames;
public boolean filterOut(SAMRecord rec) { public boolean filterOut(SAMRecord rec) {

7
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
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@ -68,6 +68,13 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
* -I input1.bam \ * -I input1.bam \
* -I input2.bam \ * -I input2.bam \
* --read_filter MappingQualityZero * --read_filter MappingQualityZero
*
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T PrintReads \
* -o output.bam \
* -I input.bam \
* -n 2000
* </pre> * </pre>
* *
*/ */