diff --git a/misc-scripts/assembly/fix_component_gaps.pl b/misc-scripts/assembly/fix_component_gaps.pl
deleted file mode 100755
index 2cd468b418d4b6ea40df4536b2159d78d1e9f5de..0000000000000000000000000000000000000000
--- a/misc-scripts/assembly/fix_component_gaps.pl
+++ /dev/null
@@ -1,267 +0,0 @@
-#!/usr/local/ensembl/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 toplevel seq_regions
-
- --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.
-
-It also merges adjacent assembly segments which can result from alternating
-alignments from clone identity and blastz alignment.
-
-=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
-<dev@ensembl.org>
-
-=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 $sql = qq(
- SELECT a.*
- FROM assembly a, seq_region sr1, seq_region sr2,
- coord_system cs1, coord_system cs2
- WHERE a.asm_seq_region_id = sr1.seq_region_id
- AND a.cmp_seq_region_id = sr2.seq_region_id
- AND sr1.coord_system_id = cs1.coord_system_id
- AND sr2.coord_system_id = cs2.coord_system_id
- AND cs1.version = '$assembly'
- AND cs2.version = '$altassembly'
- AND sr2.name = ?
- ORDER BY a.cmp_start
-);
-
-my $sth = $dbh->prepare($sql);
-
-my $fmt1 = "%10s %10s %10s %10s %3s\n";
-
-
-foreach my $chr ($support->param('chromosomes')) {
-
-
- $support->log_stamped("\nToplevel seq_region $chr...\n");
-
- $sth->execute($chr);
-
- my @rows = ();
-
- # do an initial fetch
- my $last = $sth->fetchrow_hashref;
-
- # skip seq_regions for which we don't have data
- unless ($last) {
- $support->log("No mappings found. Skipping.\n", 1);
- next;
- }
-
- push @rows, $last;
-
- my $i = 0;
- my $j = 0;
- my $k = 0;
-
- while ($last and (my $r = $sth->fetchrow_hashref)) {
- # merge adjacent assembly segments (these can result from alternating
- # alignments from clone identity and blastz alignment)
- if ($last->{'asm_end'} == ($r->{'asm_start'} - 1) and
- $last->{'cmp_end'} == ($r->{'cmp_start'} - 1)) {
-
- $j++;
-
- # debug warnings
- $support->log_verbose('merging - last: '.sprintf($fmt1,
- map { $last->{$_} } qw(asm_start asm_end cmp_start cmp_end ori)), 1);
- $support->log_verbose('this: '.sprintf($fmt1, map { $r->{$_} }
- qw(asm_start asm_end cmp_start cmp_end ori)), 1);
-
- # remove last row
- pop(@rows);
-
- # merge segments and add new row
- $last->{'asm_end'} = $r->{'asm_end'};
- $last->{'cmp_end'} = $r->{'cmp_end'};
- push @rows, $last;
-
- next;
- }
-
- # bridge small gaps (again, these can result from alternating alignments
- # from clone identity and blastz alignment). A maximum gap size of 10bp is
- # allowed
- my $asm_gap = $r->{'asm_start'} - $last->{'asm_end'} - 1;
- my $cmp_gap = $r->{'cmp_start'} - $last->{'cmp_end'} - 1;
-
- if ($asm_gap == $cmp_gap and $asm_gap <= 10 and $asm_gap > 0) {
-
- $k++;
-
- # debug warnings
- $support->log_verbose('bridging - last: '.sprintf($fmt1,
- map { $last->{$_} } qw(asm_start asm_end cmp_start cmp_end ori)), 1);
- $support->log_verbose('this: '.sprintf($fmt1, map { $r->{$_} }
- qw(asm_start asm_end cmp_start cmp_end ori)), 1);
-
- # remove last row
- pop(@rows);
-
- # merge segments and add new row
- $last->{'asm_end'} = $r->{'asm_end'};
- $last->{'cmp_end'} = $r->{'cmp_end'};
- push @rows, $last;
-
- next;
- }
-
- push @rows, $r;
- $last = $r;
- }
-
- $support->log("Merged $j mappings.\n", 1);
- $support->log("Bridged $k gaps.\n", 1);
-
- if ((!$support->param('dry_run')) && ($j + $k > 0) ) {
-
- # delete all current mappings from the db and insert the corrected ones
- my $c = $dbh->do(qq(
- DELETE a
- FROM assembly a, seq_region sr1, seq_region sr2,
- coord_system cs1, coord_system cs2
- WHERE a.asm_seq_region_id = sr1.seq_region_id
- AND a.cmp_seq_region_id = sr2.seq_region_id
- AND sr1.coord_system_id = cs1.coord_system_id
- AND sr2.coord_system_id = cs2.coord_system_id
- AND cs1.version = '$assembly'
- AND cs2.version = '$altassembly'
- AND sr2.name = '$chr'
- ));
-
- $support->log("\nDeleted $c entries from the assembly table.\n");
-
- # now insert the fixed entries
- $sql = qq(INSERT IGNORE 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));
- }
-
- $support->log("Added ".scalar(@rows)." fixed entries to the assembly table.\n");
-
- }
-
-
-}
-
-$sth->finish;
-
-
-# finish logfile
-$support->finish_log;
-