Add new option noindex to commandline help.

bin/merge_or_mark.pl

@@ -172,6 +172,8 @@ =head1 SYNOPSIS
     -nomarkdup   -n   Don't mark duplicates [flag]
     -qnamesort   -q   Use queryname sorting flag in bammerge rather than coordinate. [flag].
                       To be used in conjunction with -nomarkdup only
+    -noindex     -i   Don't attempt to index the merged file. Only available in conjunction with 
+                      -qnamesort.
     -csi              Use CSI index instead of BAI for BAM files [flag].
     -cram        -c   Output cram, see '-sc' [flag]
     -scramble    -sc  Single quoted string of parameters to pass to Scramble when '-c' used
@@ -247,6 +249,11 @@ =head2 OPTIONAL parameters
 Use queryname sorting in bammerge calls rather than the default coordinate.
 Can only be used in combination with B<-nomarkdup>
 
+=item B<-noindex>
+
+Don't attempt to generate an index for the merged file.
+Can only be used in combination with B<-qnamesort>
+
 =item B<-cram>
 
 Final output file will be a CRAM file instead of BAM.  To tune the the compression methods see then