From fd1831b4a520e68b15b6b5b958aa2d04ade4e287 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 15 Sep 2011 16:25:03 -0400
Subject: [PATCH] Updating docs to include more details

---
 .../gatk/walkers/fasta/FastaAlternateReferenceWalker.java   | 6 ++++--
 .../sting/gatk/walkers/fasta/FastaReferenceWalker.java      | 3 +++
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
index fd912334f..4e2c17bf6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
@@ -43,8 +43,10 @@ import java.util.List;
  * Generates an alternative reference sequence over the specified interval.
  *
  * <p>
- * Given variant ROD tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s).
- * Additionally, allows for a "snpmask" ROD to set overlapping bases to 'N'.
+ * Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s).
+ * Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'.
+ * Note that if there are multiple variants at a site, it takes the first one seen.
+ * Reference bases for each interval will be output as a separate fasta sequence (named numerically in order).
  *
  * <h2>Input</h2>
  * <p>
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
index 5f3b37cc8..7ae5c5c75 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
@@ -42,6 +42,9 @@ import java.io.PrintStream;
  *
  * <p>
  * The output format can be partially controlled using the provided command-line arguments.
+ * Specify intervals with the usual -L argument to output only the reference bases within your intervals.
+ * Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a
+ * separate fasta sequence (named numerically in order).
  *
  * <h2>Input</h2>
  * <p>