added some more comprehensive RepeatMaskedSlice tests that were not in slice.t

modules/t/repeatMaskedSlice.t

+use strict;
+use warnings;
+
+use lib 't';
+
+
+BEGIN { $| = 1;
+	use Test;
+	plan tests => 6;
+}
+
+use TestUtils qw( debug );
+
+use Bio::EnsEMBL::RepeatMaskedSlice;
+
+use MultiTestDB;
+
+our $verbose = 0;
+
+my $multi = MultiTestDB->new();
+my $db    = $multi->get_DBAdaptor('core');
+
+
+my $slice_adaptor = $db->get_SliceAdaptor();
+
+my $slice = $slice_adaptor->fetch_by_region('chromosome', '20');
+
+my $rm_slice = Bio::EnsEMBL::RepeatMaskedSlice->new
+  (-START             => 30_980_001,
+   -END               => 30_980_100,
+   -STRAND            => 1,
+   -ADAPTOR           => $slice_adaptor,
+   -SEQ_REGION_NAME   => '20',
+   -SEQ_REGION_LENGTH => $slice->seq_region_length(),
+   -COORD_SYSTEM      => $slice->coord_system(),
+   -SOFT_MASK         => 0);
+
+
+my $seq = $rm_slice->seq();
+ok(length($seq) == 100);
+
+debug("rm_slice->seq           = $seq");
+
+my $subseq = $rm_slice->subseq(2,100);
+ok(length($subseq) == 99);
+debug("rm_slice->subseq(2,100) =  $subseq");
+ok($subseq eq substr($seq, 1));
+
+
+$rm_slice = Bio::EnsEMBL::RepeatMaskedSlice->new
+  (-START             => 30_980_001,
+   -END               => 30_980_100,
+   -STRAND            => 1,
+   -ADAPTOR           => $slice_adaptor,
+   -SEQ_REGION_NAME   => '20',
+   -SEQ_REGION_LENGTH => $slice->seq_region_length(),
+   -COORD_SYSTEM      => $slice->coord_system(),
+   -SOFT_MASK         => 1);
+
+my $sm_seq = $rm_slice->seq();
+
+my $normal_seq = $slice->subseq(30_980_001,30_980_100);
+
+#check that uppercasing softmasked makes the same sequence as non masked
+ok(uc($sm_seq) eq $normal_seq && $sm_seq ne $normal_seq);
+
+#check that replacing lowercase with Ns gives hardmasked
+$sm_seq =~ tr/[a-z]/N/;
+ok($sm_seq eq $seq);
+
+#
+# make sure everything works on negative strand too
+#
+$rm_slice = Bio::EnsEMBL::RepeatMaskedSlice->new
+  (-START             => 30_980_001,
+   -END               => 30_980_100,
+   -STRAND            => -1,
+   -ADAPTOR           => $slice_adaptor,
+   -SEQ_REGION_NAME   => '20',
+   -SEQ_REGION_LENGTH => $slice->seq_region_length(),
+   -COORD_SYSTEM      => $slice->coord_system(),
+   -SOFT_MASK         => 0);
+
+
+$seq = $rm_slice->seq();
+debug("(-ve) rm_slice->seq           = $seq");
+
+$subseq = $rm_slice->subseq(2,100);
+debug("(-ve) rm_slice->subseq(2,100) =  $subseq");
+ok($subseq eq substr($seq, 1));