don't limit seq_region to chromosomes, so the script can be used to fix...

don't limit seq_region to chromosomes, so the script can be used to fix overlaps in mappings between other coord_systems

misc-scripts/assembly/fix_overlaps.pl

-#!/usr/local/ensembl/bin/perl
+#!/usr/bin/env perl
 
 =head1 NAME
 
-fix_overlaps.pl - remove overlapping mappings between two closely related
-assemblies
+fix_overlaps.pl - remove overlapping mappings in the assembly coordinates (asm_start - asm_end) between two closely related assemblies 
 
 =head1 SYNOPSIS
 
@@ -19,11 +18,10 @@ Required arguments:
   --assembly=ASSEMBLY                 assembly version ASSEMBLY
 
   --altassembly=ASSEMBLY              alternative assembly version ASSEMBLY
+  --chromosomes, --chr=LIST           only process LIST seq_regions
 
 Optional arguments:
 
-  --chromosomes, --chr=LIST           only process LIST toplevel seq_regions
-
   --conffile, --conf=FILE             read parameters from FILE
                                       (default: conf/Conversion.ini)
 
@@ -38,10 +36,9 @@ Optional arguments:
 
 =head1 DESCRIPTION
 
-This script removes overlapping mappings that were generated by the code in
-align_nonident_regions.pl. Mappings are trimmed so that no overlaps are present
-in the assembly table, because such overlaps may break the AssemblyMapper when
-projecting between the two assemblies.
+This script removes overlapping mappings from the assembly coordinates. 
+Mappings are trimmed so that such overlaps don't break the AssemblyMapper when
+projecting between the reference and non-reference assemblies.
     
 It also merges adjacent assembly segments which can result from alternating
 alignments from clone identity and blastz alignment.
@@ -114,7 +111,8 @@ $support->init_log;
 
 $support->check_required_params(
     'assembly',
-    'altassembly'
+    'altassembly',
+    'chromosomes',
 );
 
 # database connection