MBA documentation (#1922)

broadinstitute · Nov 21, 2023 · 257c1c1 · 257c1c1
1 parent 7c65e3c
commit 257c1c1
Showing 1 changed file with 7 additions and 0 deletions.
diff --git a/src/main/java/picard/sam/MergeBamAlignment.java b/src/main/java/picard/sam/MergeBamAlignment.java
@@ -73,6 +73,10 @@
  *      R=reference_sequence.fasta
  * </pre>
  *
+ * <h3>Note about required arguments</h3>
+ * 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.
+ *
  *
  * <h3>Caveats</h3>
  * This tool has been developing for a while and many arguments have been added to it over the years.
@@ -127,6 +131,9 @@ public class MergeBamAlignment extends CommandLineProgram {
             "     O=merge_alignments.bam \\\n" +
             "     R=reference_sequence.fasta\n" +
             "\n" +
+            "<h3>Note about required arguments</h3>\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." +
             "<h3>Caveats</h3>\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" +