From 3dbcf87323a8c6f526fd578f079ad8e3aa00ffe8 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Tue, 23 Aug 2011 11:43:40 +0000
Subject: [PATCH] Previous change backed out, as not in all cases 1bp slice
start = seq_region_start or slice end = seq_region_end.
---
.../Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm | 76 ++++++++-----------
1 file changed, 32 insertions(+), 44 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
index 330c01a9c2..e273e3673e 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
@@ -600,51 +600,41 @@ sub _slice_fetch {
$sr_id = $self->get_seq_region_id_external($sr_id);
$constraint .= " AND " if($constraint);
- $constraint .=
- "${tab_syn}.seq_region_id = $sr_id";
-
- #check if we're dealing with a SNP
- if ($slice_start == $slice_end)
- {
- $constraint .=
- " AND ${tab_syn}.seq_region_start = $slice_end" .
- " AND ${tab_syn}.seq_region_end = $slice_start";
+ if ( !$slice->is_circular() ) {
+ # Deal with the default case of a non-circular chromosome.
+ $constraint .=
+ "${tab_syn}.seq_region_id = $sr_id AND "
+ . "${tab_syn}.seq_region_start <= $slice_end AND "
+ . "${tab_syn}.seq_region_end >= $slice_start";
+ } else {
+ # Deal with the case of a circular chromosome.
+ if ( $slice_start > $slice_end ) {
+ $constraint .=
+ "${tab_syn}.seq_region_id = $sr_id "
+ . "AND ( ${tab_syn}.seq_region_start >= $slice_start "
+ . "OR ${tab_syn}.seq_region_start <= $slice_end "
+ . "OR ${tab_syn}.seq_region_end >= $slice_start "
+ . "OR ${tab_syn}.seq_region_end <= $slice_end "
+ . "OR ${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end)";
+
+
+ } else {
+ $constraint .=
+ "${tab_syn}.seq_region_id = $sr_id "
+ . "AND ((${tab_syn}.seq_region_start <= $slice_end "
+ . "AND ${tab_syn}.seq_region_end >= $slice_start) "
+ . "OR (${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end "
+ . "AND (${tab_syn}.seq_region_start <= $slice_end "
+ . "OR ${tab_syn}.seq_region_end >= $slice_start)))";
+ }
}
- else {
-
- if ( !$slice->is_circular() ) {
- # Deal with the default case of a non-circular chromosome.
- $constraint .=
- " AND ${tab_syn}.seq_region_start <= $slice_end"
- . " AND ${tab_syn}.seq_region_end >= $slice_start";
-
- if($max_len) {
- my $min_start = $slice_start - $max_len;
- $constraint .=
- " AND ${tab_syn}.seq_region_start >= $min_start";
- }
-
- } else {
- # Deal with the case of a circular chromosome.
- if ( $slice_start > $slice_end ) {
- $constraint .=
- " AND ( ${tab_syn}.seq_region_start >= $slice_start "
- . "OR ${tab_syn}.seq_region_start <= $slice_end "
- . "OR ${tab_syn}.seq_region_end >= $slice_start "
- . "OR ${tab_syn}.seq_region_end <= $slice_end "
- . "OR ${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end)";
-
- } else {
- $constraint .=
- " AND ((${tab_syn}.seq_region_start <= $slice_end "
- . "AND ${tab_syn}.seq_region_end >= $slice_start) "
- . "OR (${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end "
- . "AND (${tab_syn}.seq_region_start <= $slice_end "
- . "OR ${tab_syn}.seq_region_end >= $slice_start)))";
- }
- }
+ if($max_len && ! $slice->is_circular) {
+ my $min_start = $slice_start - $max_len;
+ $constraint .=
+ " AND ${tab_syn}.seq_region_start >= $min_start";
}
+
my $fs = $self->generic_fetch($constraint,undef,$slice);
@@ -1278,5 +1268,3 @@ sub remove_by_feature_id {
1;
-
-
--
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