From 97be74eb300ccf4a90187c53df20be0867dc6c6f Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Fri, 15 Sep 2006 07:48:07 +0000
Subject: [PATCH] Convert cigar line read from exonerate to format 439M after
reading.
---
misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm | 2 ++
1 file changed, 2 insertions(+)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index d8c67b9ad2..4d5a1c2c2f 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -1103,6 +1103,8 @@ sub parse_mappings {
chomp();
my ($label, $query_id, $target_id, $identity, $query_length, $target_length, $query_start, $query_end, $target_start, $target_end, $cigar_line, $score) = split(/:/, $_);
$cigar_line =~ s/ //g;
+ $cigar_line =~ s/([MDI])(\d+)/$2$1/ig;
+
if($query_id == 138110 || $query_id == 523601){
print "processing $query_id\n";
--
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