update options

art

@@ -90,22 +90,24 @@ SYNOPSIS
 USAGE
         $0 [options] <SEQUENCE_FILE> [+FEATURE_FILE ...]
 OPTIONS
-        SEQUENCE_FILE              An EMBL, GenBank, FASTA, or GFF3 file
-        FEATURE_FILE               An Artemis TAB file, or GFF file
-
-        -options FILE              Read a text file of options from FILE
-        -debug                     Run using the debugging JVM instead
-        -fast | -fast64            Use the FastVM (hp Tru64 UNIX) with 32/64 bit pointers
-
-        -Dblack_belt_mode=?        Keep warning messages to a minimum [true,false]
-        -Doffset=XXX               Open viewer at base position XXX [integer >= 1]
-        -Duserplot=FILE[,FILE2]    Open one or more userplots
-        -Dloguserplot=FILE[,FILE2] Open one or more userplots, take log(data)
-        -Dbam=FILE[,FILE2,...]     Open one or more BAM, VCF or BCF files
-        -Dshow_forward_lines=?     Hide/show forward frame lines [true,false]
-        -Dshow_reverse_lines=?     Hide/show reverse frame lines [true,false]
-        -Dchado="h:p/d?u"          Get Artemis to open this CHADO database
-        -Dread_only                Open CHADO database read-only
+        SEQUENCE_FILE                  An EMBL, GenBank, FASTA, or GFF3 file
+        FEATURE_FILE                   An Artemis TAB file, or GFF file
+
+        -options FILE                  Read a text file of options from FILE
+        -debug                         Run using the debugging JVM instead
+        -fast | -fast64                Use the FastVM (hp Tru64 UNIX) with 32/64 bit pointers
+
+        -Dblack_belt_mode=?            Keep warning messages to a minimum [true,false]
+        -Doffset=XXX                   Open viewer at base position XXX [integer >= 1]
+        -Duserplot=FILE[,FILE2]        Open one or more userplots
+        -Dloguserplot=FILE[,FILE2]     Open one or more userplots, take log(data)
+        -Dbam=FILE[,FILE2,...]         Open one or more BAM, VCF or BCF files
+        -DbamClone=n                   Open all BAMs in multiple (n > 1) panels
+        -Dbam[1,2,..]=FILE[,FILE2,..]  Open BAMs in separate panels
+        -Dshow_forward_lines=?         Hide/show forward frame lines [true,false]
+        -Dshow_reverse_lines=?         Hide/show reverse frame lines [true,false]
+        -Dchado="h:p/d?u"              Get Artemis to open this CHADO database
+        -Dread_only                    Open CHADO database read-only
 EXAMPLES
         % art AJ006275.embl 
         % art contigs.fa +annotation.gff +islands.tab