From 450ea233a51f2a12784088736e2ba03e3fa4b279 Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 11 Dec 2009 17:17:34 +0000 Subject: [PATCH] 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 --- .../broadinstitute/sting/gatk/walkers/CountLociWalker.java | 7 ++----- .../sting/gatk/walkers/CountReadsWalker.java | 6 +++++- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java index ba828616b..83a491ebd 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java @@ -5,11 +5,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; /** - * Created by IntelliJ IDEA. - * User: mdepristo - * Date: Feb 22, 2009 - * Time: 3:22:14 PM - * To change this template use File | Settings | File Templates. + * Basic example of a locus-backed analysis. Walks over the input data set, calculating the number of + * covered loci for diagnostic purposes. */ public class CountLociWalker extends LocusWalker implements TreeReducible { public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java index 3703c098e..9aa35fac8 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java @@ -1,8 +1,12 @@ package org.broadinstitute.sting.gatk.walkers; 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}) public class CountReadsWalker extends ReadWalker { public Integer map(char[] ref, SAMRecord read) {