From 3c114152fa290647a7f4c01758b5e5bfc3c4adce Mon Sep 17 00:00:00 2001
From: Kevin Howe <klh@ebi.ac.uk>
Date: Wed, 23 Mar 2005 14:43:34 +0000
Subject: [PATCH] For adjacent gaps in query and target, sanity checks
"warning"ed on the forward strand and "throw"ed on the reverse strand! Made
them both warnings.
---
modules/Bio/EnsEMBL/BaseAlignFeature.pm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/BaseAlignFeature.pm b/modules/Bio/EnsEMBL/BaseAlignFeature.pm
index 008826071b..e4759db1e0 100644
--- a/modules/Bio/EnsEMBL/BaseAlignFeature.pm
+++ b/modules/Bio/EnsEMBL/BaseAlignFeature.pm
@@ -715,9 +715,9 @@ sub _parse_features {
#sanity check, Should not be an insertion and deletion
if($insertion_flag) {
- throw("Should not be an deletion and insertion on the " .
- "same alignment region. prev2 = $prev2; f->hend() = " .
- $f->hend() . "; cigar_line = $string;\n");
+ warning("Should not be an deletion and insertion on the " .
+ "same alignment region. prev2 = $prev2; f->hend() = " .
+ $f->hend() . "; cigar_line = $string;\n");
}
}
#shift our position in the hit seq alignment
--
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