diff --git a/misc-scripts/assembly/fix_overlaps.pl b/misc-scripts/assembly/fix_overlaps.pl
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+++ b/misc-scripts/assembly/fix_overlaps.pl
@@ -0,0 +1,233 @@
+#!/software/bin/perl
+
+=head1 NAME
+
+fix_overlaps.pl - remove overlapping mappings between two closely related
+assemblies
+
+=head1 SYNOPSIS
+
+fix_overlaps.pl [arguments]
+
+Required arguments:
+
+ --dbname, db_name=NAME database name NAME
+ --host, --dbhost, --db_host=HOST database host HOST
+ --port, --dbport, --db_port=PORT database port PORT
+ --user, --dbuser, --db_user=USER database username USER
+ --pass, --dbpass, --db_pass=PASS database passwort PASS
+ --assembly=ASSEMBLY assembly version ASSEMBLY
+
+ --altassembly=ASSEMBLY alternative assembly version ASSEMBLY
+
+Optional arguments:
+
+ --chromosomes, --chr=LIST only process LIST chromosomes
+
+ --conffile, --conf=FILE read parameters from FILE
+ (default: conf/Conversion.ini)
+
+ --logfile, --log=FILE log to FILE (default: *STDOUT)
+ --logpath=PATH write logfile to PATH (default: .)
+ --logappend, --log_append append to logfile (default: truncate)
+
+ -v, --verbose=0|1 verbose logging (default: false)
+ -i, --interactive=0|1 run script interactively (default: true)
+ -n, --dry_run, --dry=0|1 don't write results to database
+ -h, --help, -? print help (this message)
+
+=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.
+
+=head1 RELATED FILES
+
+The whole process of creating a whole genome alignment between two assemblies
+is done by a series of scripts. Please see
+
+ ensembl/misc-scripts/assembly/README
+
+for a high-level description of this process, and POD in the individual scripts
+for the details.
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence:
+Please see http://www.ensembl.org/code_licence.html for details
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use FindBin qw($Bin);
+use Getopt::Long;
+use Pod::Usage;
+use Bio::EnsEMBL::Utils::ConversionSupport;
+
+$| = 1;
+
+my $support = new Bio::EnsEMBL::Utils::ConversionSupport("$Bin/../../..");
+
+# parse options
+$support->parse_common_options(@_);
+$support->parse_extra_options(
+ 'assembly=s',
+ 'altassembly=s',
+ 'chromosomes|chr=s@',
+);
+$support->allowed_params(
+ $support->get_common_params,
+ 'assembly',
+ 'altassembly',
+ 'chromosomes',
+);
+
+if ($support->param('help') or $support->error) {
+ warn $support->error if $support->error;
+ pod2usage(1);
+}
+
+$support->comma_to_list('chromosomes');
+
+# ask user to confirm parameters to proceed
+$support->confirm_params;
+
+# get log filehandle and print heading and parameters to logfile
+$support->init_log;
+
+$support->check_required_params(
+ 'assembly',
+ 'altassembly'
+);
+
+# database connection
+my $dba = $support->get_database('ensembl');
+my $dbh = $dba->dbc->db_handle;
+
+my $assembly = $support->param('assembly');
+my $altassembly = $support->param('altassembly');
+
+my $sql = qq(
+ SELECT a.*
+ FROM assembly a, seq_region sr1, seq_region sr2,
+ coord_system cs1, coord_system cs2
+ WHERE a.asm_seq_region_id = sr1.seq_region_id
+ AND a.cmp_seq_region_id = sr2.seq_region_id
+ AND sr1.coord_system_id = cs1.coord_system_id
+ AND sr2.coord_system_id = cs2.coord_system_id
+ AND cs1.name = 'chromosome'
+ AND cs2.name = 'chromosome'
+ AND cs1.version = '$assembly'
+ AND cs2.version = '$altassembly'
+ AND sr1.name = ?
+ ORDER BY a.asm_start
+);
+
+my $sth = $dbh->prepare($sql);
+
+my $fmt1 = "%10s %10s %10s %10s %3s\n";
+my @rows = ();
+
+foreach my $chr ($support->sort_chromosomes) {
+ $support->log_stamped("\nChromosome $chr...\n");
+
+ $sth->execute($chr);
+
+ # do an initial fetch
+ my $last = $sth->fetchrow_hashref;
+ push @rows, $last;
+
+ my $i = 0;
+
+ while ($last and (my $r = $sth->fetchrow_hashref)) {
+ # look for overlaps with last segment
+ if ($last->{'asm_end'} >= $r->{'asm_start'}) {
+
+ $i++;
+
+ # debug warnings
+ $support->log_verbose('last: '.sprintf($fmt1, map { $last->{$_} }
+ qw(asm_start asm_end cmp_start cmp_end ori)), 1);
+ $support->log_verbose('before: '.sprintf($fmt1, map { $r->{$_} }
+ qw(asm_start asm_end cmp_start cmp_end ori)), 1);
+
+ # skip if this segment ends before the last one
+ if ($r->{'asm_end'} <= $last->{'asm_end'}) {
+ $support->log_verbose("skipped\n\n", 1);
+ next;
+ }
+
+ my $overlap = $last->{'asm_end'} - $r->{'asm_start'} + 1;
+
+ $r->{'asm_start'} += $overlap;
+
+ if ($r->{'ori'} == -1) {
+ $r->{'cmp_end'} -= $overlap;
+ } else {
+ $r->{'cmp_start'} += $overlap;
+ }
+
+ $support->log_verbose('after: '.sprintf($fmt1, map { $r->{$_} }
+ qw(asm_start asm_end cmp_start cmp_end ori))."\n", 1);
+ }
+
+ push @rows, $r;
+ $last = $r;
+ }
+
+ $support->log("Fixed $i mappings.\n", 1);
+}
+
+$sth->finish;
+
+# fix the assembly table
+if ($support->param('dry_run')) {
+ $support->log("\nNothing else to do for a dry run.\n");
+} else {
+
+ # delete all current mappings from the db and insert the corrected ones
+ my $c = $dbh->do(qq(
+ DELETE a
+ FROM assembly a, seq_region sr1, seq_region sr2,
+ coord_system cs1, coord_system cs2
+ WHERE a.asm_seq_region_id = sr1.seq_region_id
+ AND a.cmp_seq_region_id = sr2.seq_region_id
+ AND sr1.coord_system_id = cs1.coord_system_id
+ AND sr2.coord_system_id = cs2.coord_system_id
+ AND cs1.name = 'chromosome'
+ AND cs2.name = 'chromosome'
+ AND cs1.version = '$assembly'
+ AND cs2.version = '$altassembly'
+ ));
+ $support->log("\nDeleted $c entries from the assembly table.\n");
+
+ # now insert the fixed entries
+ $sql = qq(INSERT INTO assembly VALUES (?, ?, ?, ?, ?, ?, ?));
+ my $sth1 = $dbh->prepare($sql);
+
+ foreach my $r (@rows) {
+ $sth1->execute(map { $r->{$_} } qw(asm_seq_region_id cmp_seq_region_id
+ asm_start asm_end cmp_start cmp_end ori));
+ }
+
+ $support->log("Added ".scalar(@rows)." fixed entries to the assembly table.\n");
+}
+
+
+# finish logfile
+$support->finish_log;
+