From 55e1fe74541c9902618f289cada4638bd28bf543 Mon Sep 17 00:00:00 2001 From: Chris Kachulis Date: Mon, 20 Nov 2023 13:24:14 -0500 Subject: [PATCH 1/2] documentation --- src/main/java/picard/sam/MergeBamAlignment.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/main/java/picard/sam/MergeBamAlignment.java b/src/main/java/picard/sam/MergeBamAlignment.java index 7eb2c1de4c..4d9fc32681 100644 --- a/src/main/java/picard/sam/MergeBamAlignment.java +++ b/src/main/java/picard/sam/MergeBamAlignment.java @@ -73,6 +73,10 @@ * R=reference_sequence.fasta * * + *

Note about required arguments

+ * The aligned reads must be specified using either the ALIGNED_BAM or READ1_ALIGNED_BAM and READ2_ALIGNED_BAM arguments. + * Without aligned reads specified in one of those manners, the tool will not run. + * * *

Caveats

* This tool has been developing for a while and many arguments have been added to it over the years. From 216ffa9cf360b0a0ded0ea6ca19c94d6b6cc5353 Mon Sep 17 00:00:00 2001 From: Chris Kachulis Date: Mon, 20 Nov 2023 13:26:21 -0500 Subject: [PATCH 2/2] documentation --- src/main/java/picard/sam/MergeBamAlignment.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/main/java/picard/sam/MergeBamAlignment.java b/src/main/java/picard/sam/MergeBamAlignment.java index 4d9fc32681..8ea788277e 100644 --- a/src/main/java/picard/sam/MergeBamAlignment.java +++ b/src/main/java/picard/sam/MergeBamAlignment.java @@ -131,6 +131,9 @@ public class MergeBamAlignment extends CommandLineProgram { " O=merge_alignments.bam \\\n" + " R=reference_sequence.fasta\n" + "\n" + + "

Note about required arguments

\n" + + " The aligned reads must be specified using either the ALIGNED_BAM or READ1_ALIGNED_BAM and READ2_ALIGNED_BAM arguments. " + + " Without aligned reads specified in one of those manners, the tool will not run." + "

Caveats

\n" + "This tool has been developing for a while and many arguments have been added to it over the years. " + "You may be particularly interested in the following (partial) list:\n" +