From 1ef8a1750a4821cdafd109b63dd83e62b873b68e Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 6 Sep 2011 21:07:49 -0400
Subject: [PATCH] I asked nicely and got nothing.  Then I threatened and still
 got nothing.  So I am carrying through on my threats.  Guillermo, you have a
 short reprieve because you were away on vacation, but let's get yours done
 tomorrow afternoon.

---
 .../sting/gatk/walkers/coverage/DepthOfCoverageWalker.java   | 3 +++
 .../gatk/walkers/indels/SomaticIndelDetectorWalker.java      | 5 +++++
 .../sting/gatk/walkers/validation/ValidationAmplicons.java   | 3 +++
 3 files changed, 11 insertions(+)

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 7fe16c9df..4537f06f8 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
@@ -60,6 +60,9 @@ import java.util.*;
  * and/or percentage of bases covered to or beyond a threshold.
  * Additionally, reads and bases can be filtered by mapping or base quality score.
  *
+ * <b>If any of the command-line arguments for this tool are not clear to you,
+ * please email chartl at broadinstitute dot org and he will gladly explain them in more detail.</b>
+ *
  * <h2>Input</h2>
  * <p>
  * One or more bam files (with proper headers) to be analyzed for coverage statistics
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
index 546bbe1a6..e5ad3106d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
@@ -77,6 +77,11 @@ import java.util.*;
  * if even a weak evidence for the same indel, not necessarily a confident call, exists in the first sample ("Normal"), or as somatic
  * if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains
  * only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
+ *
+ * <b>If any of the general usage of this tool or any of the command-line arguments for this tool are not clear to you,
+ * please email asivache at broadinstitute dot org and he will gladly explain everything in more detail.</b>
+ *
+ *
  */
 @ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class})
 public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
index f9bd019ea..178b4c177 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
@@ -39,6 +39,9 @@ import java.util.List;
  * reasons why the site may fail validation (nearby variation, for example).
  * </p>
  *
+ * <b>If any of the command-line arguments for this tool are not clear to you,
+ * please email chartl at broadinstitute dot org and he will gladly explain them in more detail.</b>
+ *
  * <h2>Input</h2>
  * <p>
  * Requires a VCF containing alleles to design amplicons towards, a VCF of variants to mask out of the amplicons, and an