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ensembl-gh-mirror
ensembl
Commits
3eb40c77
Commit
3eb40c77
authored
Feb 23, 2010
by
William McLaren
Browse files
Include read coverage filtering for sequence
parent
72fcd640
Changes
1
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-1
modules/Bio/EnsEMBL/MappedSlice.pm
modules/Bio/EnsEMBL/MappedSlice.pm
+4
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modules/Bio/EnsEMBL/MappedSlice.pm
View file @
3eb40c77
...
...
@@ -535,7 +535,10 @@ sub seq {
# get slice/mapper pairs from mapped slice (usually only one anyway)
foreach
my
$pair
(
@
{
$self
->
get_all_Slice_Mapper_pairs
()})
{
my
(
$s
,
$m
)
=
@$pair
;
my
$seq
=
$s
->
seq
();
# make sure to send extra args
# eg strain slices might need read coverage filtering
my
$seq
=
$s
->
seq
(
@
_
);
# project from mapped slice to reference slice using the mapper
foreach
my
$ref_coord
(
$m
->
map_coordinates
('
mapped_slice
',
1
,
CORE::
length
(
$seq
),
$s
->
strand
,
'
mapped_slice
'))
{
...
...
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