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Docs for the basic walkers: CountLoci, CountReads. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2326 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2009-12-11 17:17:34 +00:00
parent f97ac939fa
commit 450ea233a5
2 changed files with 7 additions and 6 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java
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@ -5,11 +5,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
/** /**
* Created by IntelliJ IDEA. * Basic example of a locus-backed analysis. Walks over the input data set, calculating the number of
* User: mdepristo * covered loci for diagnostic purposes.
* Date: Feb 22, 2009
* Time: 3:22:14 PM
* To change this template use File | Settings | File Templates.
*/ */
public class CountLociWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> { public class CountLociWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {

6
java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java
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@ -1,8 +1,12 @@
package org.broadinstitute.sting.gatk.walkers; package org.broadinstitute.sting.gatk.walkers;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
/**
* Basic example of a read-backed analysis. Walks over the input data set, calculating the number of
* reads seen for diagnostic purposes. Can also count the number of reads matching a given criterion using
* read filters (see the --read-filter command line argument).
*/
@Requires({DataSource.READS, DataSource.REFERENCE}) @Requires({DataSource.READS, DataSource.REFERENCE})
public class CountReadsWalker extends ReadWalker<Integer, Integer> { public class CountReadsWalker extends ReadWalker<Integer, Integer> {
public Integer map(char[] ref, SAMRecord read) { public Integer map(char[] ref, SAMRecord read) {