From ab0b56ed11611c1c5dc9292f2184170573bf1f44 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 16 Aug 2011 12:55:45 -0400
Subject: [PATCH] Minor doc fixes

---
 .../org/broadinstitute/sting/commandline/Output.java   |  2 +-
 .../sting/gatk/walkers/indels/IndelRealigner.java      | 10 +++++-----
 .../gatk/walkers/indels/RealignerTargetCreator.java    | 10 +++++-----
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/commandline/Output.java b/public/java/src/org/broadinstitute/sting/commandline/Output.java
index 22565dbf5..f8aef0355 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/Output.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/Output.java
@@ -55,7 +55,7 @@ public @interface Output {
      * --help argument is specified.
      * @return Doc string associated with this command-line argument.
      */
-    String doc() default "An output file presented to the walker.  Will overwrite contents if file exists.";
+    String doc() default "An output file created by the walker.  Will overwrite contents if file exists";
 
     /**
      * Is this argument required.  If true, the command-line argument system will
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 0f1c0dd3b..029b6deaf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -84,7 +84,7 @@ import java.util.*;
  *     </ol>
  *     <p>
  * An important note: the input bam(s), reference, and known indel file(s) should be the same ones used for the RealignerTargetCreator step.
- *
+ * <p>
  * Another important note: because reads produced from the 454 technology inherently contain false indels, the realigner will not currently work with them
  * (or with reads from similar technologies).
  *
@@ -101,11 +101,11 @@ import java.util.*;
  * <h2>Examples</h2>
  * <pre>
  * java -Xmx4g -jar GenomeAnalysisTK.jar \
- *   -I <input.bam> \
- *   -R <ref.fasta> \
+ *   -I input.bam \
+ *   -R ref.fasta \
  *   -T IndelRealigner \
- *   -targetIntervals <intervalListFromRTC.intervals> \
- *   -o <realignedBam.bam> \
+ *   -targetIntervals intervalListFromRTC.intervals \
+ *   -o realignedBam.bam \
  *   [--known /path/to/indels.vcf] \
  *   [-compress 0]    (this argument recommended to speed up the process *if* this is only a temporary file; otherwise, use the default value)
  * </pre>
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index 7b654e3f8..08ed1af52 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -52,7 +52,7 @@ import java.util.Collections;
 import java.util.List;
 
 /**
- * Emits intervals for the Local Indel Realigner to target for cleaning.
+ * Emits intervals for the Local Indel Realigner to target for realignment.
  *
  * <p>
  * The local realignment tool is designed to consume one or more BAM files and to locally realign reads such that the number of mismatching bases
@@ -72,7 +72,7 @@ import java.util.List;
  *     </ol>
  *     <p>
  * An important note: the input bam(s), reference, and known indel file(s) should be the same ones to be used for the IndelRealigner step.
- *
+ * <p>
  * Another important note: because reads produced from the 454 technology inherently contain false indels, the realigner will not currently work with them
  * (or with reads from similar technologies).   This tool also ignores MQ0 reads and reads with consecutive indel operators in the CIGAR string.
  *
@@ -89,10 +89,10 @@ import java.util.List;
  * <h2>Examples</h2>
  * <pre>
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
- *   -I <input.bam> \
- *   -R <ref.fasta> \
+ *   -I input.bam \
+ *   -R ref.fasta \
  *   -T RealignerTargetCreator \
- *   -o <forIndelRealigner.intervals> \
+ *   -o forIndelRealigner.intervals \
  *   [--known /path/to/indels.vcf]
  * </pre>
  *