From bd2caa0446cfbfddbf7088ee00bdf2389170477e Mon Sep 17 00:00:00 2001
From: tfenne <tfenne@tfenne.com>
Date: Mon, 19 Jun 2017 10:13:16 -0400
Subject: [PATCH 1/2] Small documentation update to BedToIntervalList.

---
 src/main/java/picard/util/BedToIntervalList.java | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/main/java/picard/util/BedToIntervalList.java b/src/main/java/picard/util/BedToIntervalList.java
index 886a40e5d..cdfdd117c 100644
--- a/src/main/java/picard/util/BedToIntervalList.java
+++ b/src/main/java/picard/util/BedToIntervalList.java
@@ -64,9 +64,16 @@
             "     -Strand - Indicates +/- strand for the interval (either + or -) <br /> " +
             "     -Interval name - (Each interval should have a unique name) " +
             "</pre>" +
-            "  <br /><br />" +
-            "This tool requires sequence dictionary file (with \".dict\" extension), which can be created from a reference sequence " +
-            "using Picard's CreateSequenceDictionary tool."+
+            "<br/>" +
+            "This tool requires sequence dictionary, provided with the SEQUENCE_DICTIONARY or SD argument. " +
+            "This argument can be any of:" +
+            "<pre>" +
+            "    - A file with .dict extension generated using Picard's CreateSequenceDictionaryTool</br>" +
+            "    - A <name>.fa or <name>.fasta file with a <name>.dict in the same directory</br>" +
+            "    - Another IntervalList that contains the dictionary to use</br>" +
+            "    - A VCF that contains #contig lines from which to generate a sequence dictionary</br>" +
+            "    - A SAM or BAM file with @SQ lines in the header from which to create a dictionary</br>" +
+            "</pre>" +
             "<h4>Usage example:</h4>" +
             "<pre>" +
             "java -jar picard.jar BedToIntervalList \\<br />" +
@@ -80,7 +87,8 @@
     @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The input BED file")
     public File INPUT;
 
-    @Option(shortName = StandardOptionDefinitions.SEQUENCE_DICTIONARY_SHORT_NAME, doc = "The sequence dictionary")
+    @Option(shortName = StandardOptionDefinitions.SEQUENCE_DICTIONARY_SHORT_NAME,
+            doc = "The sequence dictionary, or BAM/VCF/IntervalList from which a dictionary can be extracted.")
     public File SEQUENCE_DICTIONARY;
 
     @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "The output Picard Interval List")

From 51cd8ee9a43e5aba961e41215fec14a0201c6ae1 Mon Sep 17 00:00:00 2001
From: tfenne <tfenne@tfenne.com>
Date: Mon, 19 Jun 2017 13:15:43 -0400
Subject: [PATCH 2/2] Review fixup.

---
 src/main/java/picard/util/BedToIntervalList.java | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/java/picard/util/BedToIntervalList.java b/src/main/java/picard/util/BedToIntervalList.java
index cdfdd117c..5170c100a 100644
--- a/src/main/java/picard/util/BedToIntervalList.java
+++ b/src/main/java/picard/util/BedToIntervalList.java
@@ -65,14 +65,14 @@
             "     -Interval name - (Each interval should have a unique name) " +
             "</pre>" +
             "<br/>" +
-            "This tool requires sequence dictionary, provided with the SEQUENCE_DICTIONARY or SD argument. " +
-            "This argument can be any of:" +
+            "This tool requires a sequence dictionary, provided with the SEQUENCE_DICTIONARY or SD argument. " +
+            "The value given to this argument can be any of the following:" +
             "<pre>" +
             "    - A file with .dict extension generated using Picard's CreateSequenceDictionaryTool</br>" +
-            "    - A <name>.fa or <name>.fasta file with a <name>.dict in the same directory</br>" +
-            "    - Another IntervalList that contains the dictionary to use</br>" +
+            "    - A reference.fa or reference.fasta file with a reference.dict in the same directory</br>" +
+            "    - Another IntervalList with @SQ lines in the header from which to generate a dictionary</br>" +
             "    - A VCF that contains #contig lines from which to generate a sequence dictionary</br>" +
-            "    - A SAM or BAM file with @SQ lines in the header from which to create a dictionary</br>" +
+            "    - A SAM or BAM file with @SQ lines in the header from which to generate a dictionary</br>" +
             "</pre>" +
             "<h4>Usage example:</h4>" +
             "<pre>" +