From 590aeee7d2bd5d483657058d0285db553c948a35 Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 11 Dec 2009 18:15:40 +0000 Subject: [PATCH] Documentation for more basic walkers. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2329 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/coverage/DepthOfCoverageWalker.java | 4 +++- .../sting/gatk/walkers/fasta/BamToFastqWalker.java | 6 ++++-- .../sting/gatk/walkers/fasta/FastaReferenceWalker.java | 6 ++++-- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index 7be290f8a..0141539c3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java @@ -36,7 +36,9 @@ import net.sf.samtools.SAMReadGroupRecord; import java.util.*; /** - * Display the depth of coverage at a given locus. + * Computes the depth of coverage at all loci in the specified region of the reference. Includes features to control + * grouping of results by read group or by sample, or filtering loci with either a small number of overlapping alignments + * or with alignments of poor mapping quality. Can optionally include individual base counts at each locus. */ @By(DataSource.REFERENCE) public class DepthOfCoverageWalker extends LocusWalker { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java index 62f51070c..8ab68f532 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java @@ -8,8 +8,10 @@ import net.sf.samtools.SAMRecord; import java.io.*; -// create a fastq file from a bam file - +/** + * Converts reads from the input BAM file into fastq format, stripping away all alignment information. + * Optionally re-reverses the negative strand alignments using the --re-reverse command-line argument. + */ @WalkerName("BamToFastq") public class BamToFastqWalker extends ReadWalker { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java index 165f2b423..3024cf4fe 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java @@ -10,8 +10,10 @@ import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.cmdLine.Argument; -// create a fasta sequence file from a reference and intervals - +/** + * Renders a new reference in FASTA format consisting of only those loci provided in the input data set. Has optional + * features to control the output format. + */ @WalkerName("FastaReferenceMaker") public class FastaReferenceWalker extends RefWalker, GenomeLoc> { @Argument(fullName="lineWidth", shortName="lw", doc="Maximum length of sequence to write per line", required=false) public int fastaLineWidth=60;