From 034b8685889a879eda0e7c1a001358a26845755a Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Mon, 19 Sep 2011 12:16:07 -0400
Subject: [PATCH] Revert "Fix the -T argument in the DepthOfCoverage docs"

This reverts commit 0994efda998cf3a41b1a43696dbc852a441d5316.
---
 .../coverage/DepthOfCoverageWalker.java       |  9 +++----
 .../utils/codecs/refseq/RefSeqCodec.java      | 24 ++++---------------
 2 files changed, 7 insertions(+), 26 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
index 664c319ab..86f97a36c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
@@ -63,12 +63,9 @@ import java.util.*;
  * <h2>Input</h2>
  * <p>
  * One or more bam files (with proper headers) to be analyzed for coverage statistics
+ * (Optional) A REFSEQ Rod to aggregate coverage to the gene level
  * </p>
- * <p>
- *(Optional) A REFSEQ Rod to aggregate coverage to the gene level
- * <p>
- * (for information about creating the REFSEQ Rod, please consult the RefSeqCodec documentation)
- *</p></p>
+ *
  * <h2>Output</h2>
  * <p>
  * Tables pertaining to different coverage summaries. Suffix on the table files declares the contents:
@@ -96,7 +93,7 @@ import java.util.*;
  * <pre>
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
  *   -R ref.fasta \
- *   -T DepthOfCoverage \
+ *   -T VariantEval \
  *   -o file_name_base \
  *   -I input_bams.list
  *   [-geneList refSeq.sorted.txt] \
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
index f142fa5aa..d94d9ff84 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
@@ -12,35 +12,19 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import java.util.ArrayList;
 
 /**
- * Allows for reading in RefSeq information
+ * TODO FOR CHRIS HARTL
  *
  * <p>
- * Parses a sorted UCSC RefSeq file (see below) into relevant features: the gene name, the unique gene name (if multiple transcrips get separate entries), exons, gene start/stop, coding start/stop,
- * strandedness of transcription. 
+ * Codec Description
  * </p>
  *
  * <p>
- * Instructions for generating a RefSeq file for use with the RefSeq codec can be found on the Wiki here
- * <a href="http://www.broadinstitute.org/gsa/wiki/index.php/RefSeq">http://www.broadinstitute.org/gsa/wiki/index.php/RefSeq</a>
+ * See also: link to file specification
  * </p>
- * <h2> Usage </h2>
- * The RefSeq Rod can be bound as any other rod, and is specified by REFSEQ, for example
- * <pre>
- * -refSeqBinding:REFSEQ /path/to/refSeq.txt
- * </pre>
- *
- * You will need to consult individual walkers for the binding name ("refSeqBinding", above)
  *
  * <h2>File format example</h2>
- * If you want to define your own file for use, the format is (tab delimited):
- * bin, name, chrom, strand, transcription start, transcription end, coding start, coding end, num exons, exon starts, exon ends, id, alt. name, coding start status (complete/incomplete), coding end status (complete,incomplete)
- * and exon frames, for example:
- * <pre>
- * 76 NM_001011874 1 - 3204562 3661579 3206102 3661429 3 3204562,3411782,3660632, 3207049,3411982,3661579, 0 Xkr4 cmpl cmpl 1,2,0,
- * </pre>
- * for more information see <a href="http://skip.ucsc.edu/cgi-bin/hgTables?hgsid=5651&hgta_doSchemaDb=mm8&hgta_doSchemaTable=refGene">here</a>
  * <p>
- *     
+ *     A BAM file containing <b>exactly one sample</b>.
  * </p>
  *
  * @author Mark DePristo