Index: t/CoordinateMapper.t
===================================================================
--- t/CoordinateMapper.t	(revision 14857)
+++ t/CoordinateMapper.t	(working copy)
@@ -7,7 +7,7 @@
     use lib 't/lib';
 	use BioperlTest;
 	
-	test_begin(-tests => 175);
+	test_begin(-tests => 179);
 	
 	use_ok('Bio::Location::Simple');
 	use_ok('Bio::Coordinate::Pair');
@@ -359,10 +359,18 @@
 is $res->match->end, 5;
 
 # match more than two
-$pos = Bio::Location::Simple->new (-start => 5, -end => 19 );
+my @testres = (
+	     ['gene', 2, 4, undef],
+	     ['gene', 10, 14, undef],
+	     ['gene', 20, 20, undef]
+);
+
+$pos = Bio::Location::Simple->new (-start => 2, -end => 20 );
 ok $res = $transcribe->map($pos);
-is $res->each_gap, 2;
+is $res->each_gap, 3;
 is $res->each_match, 2;
+my @res =  $res->each_gap;
+compare (shift @res, shift @testres);
 
 
 
@@ -393,7 +401,7 @@
 $transcribe->add_mapper($pair1);
 $transcribe->add_mapper($pair2);
 ok $transcribe->sort;
-my @res;
+@res = ();
 map {push @res, $_->in->start } $transcribe->each_mapper;
 ok compare_arrays ([5, 15, 25], \@res);
 
@@ -418,7 +426,7 @@
 is $res->match->seq_id, '627012';
 
 ## now a split coord
-my @testres = (
+@testres = (
 	     [314696, 31917, 31937, -1],
 	     [341, 126, 59773, -1],
 	     [315843, 5332, 5963, +1]
@@ -433,7 +441,7 @@
 ## now a simple gap
 @testres = (
 	    [627011, 7447, 7507, +1],
-	    ["chr1", 273762, 273781, 1]
+	    ["chr1", 273762, 273781, undef]
 	   );
 $pos = Bio::Location::Simple->new (-start => 273701, -end => 273781, -strand => 1);
 $res = $mapper->map($pos);
@@ -547,6 +555,7 @@
 }
 
 
+use Carp;
 sub compare {
     my ($match, $test) = @_;
     is $match->seq_id eq $test->[0], 1,
Index: Bio/Coordinate/Collection.pm
===================================================================
--- Bio/Coordinate/Collection.pm	(revision 14857)
+++ Bio/Coordinate/Collection.pm	(working copy)
@@ -96,6 +96,7 @@
 # Object preamble - inherits from Bio::Root::Root
 use Bio::Coordinate::Result;
 use Bio::Coordinate::Result::Gap;
+use Set::IntSpan;
 
 use base qw(Bio::Root::Root Bio::Coordinate::MapperI);
 
@@ -323,6 +324,8 @@
    my ($self,$value) = @_;
 
    my $result = Bio::Coordinate::Result->new(-is_remote=>1);
+   my $gaps = Set::IntSpan->new($value->start . '-' . $value->end);
+   my $gap_seq_id;		# place to stash seq_id of "in" for later.
 
 IDMATCH: {
 
@@ -342,10 +345,30 @@
 	   last if $pair->in->start > $value->end;
 
 	   my $subres = $pair->map($value);
+
+	   my $gaps_for_this_pair = Set::IntSpan->new();
+	   map {
+	       $gaps_for_this_pair->U($_->start() . '-' . $_->end());
+	       $gap_seq_id = $_->seq_id;
+	   } $subres->each_gap();
+	   $gaps->I($gaps_for_this_pair) if ( $gaps_for_this_pair );
+
+	   $subres->purge_gaps();
 	   $result->add_result($subres);
        }
    }
 
+   foreach my $span ($gaps->spans()) {
+       my $gap = Bio::Coordinate::Result::Gap->new(-start => $span->[0],
+						   -end => $span->[1],
+						   -location_type =>
+						   $value->location_type
+					   );
+       $gap->seq_id($gap_seq_id) if defined $gap_seq_id;
+
+       $result->add_sub_Location($gap);
+   }
+
    $result->seq_id($result->match->seq_id) if $result->match;
    unless ($result->each_Location) {
        #build one gap;
Index: Build.PL
===================================================================
--- Build.PL	(revision 14857)
+++ Build.PL	(working copy)
@@ -30,7 +30,8 @@
                             'IO::String'                => 0,
                             'DB_File'                   => 0,
                             'Data::Stag'                => 0.10, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
-                            'Scalar::Util'              => 0 # not in Perl 5.6.1, arrived in core in 5.7.3
+                            'Scalar::Util'              => 0, # not in Perl 5.6.1, arrived in core in 5.7.3
+			    'Set::IntSpan'              => 1.13,
                            },
     build_requires      => {
                             'Test::More'                => 0,