Commit f8bc5b3e authored by Stephen Searle's avatar Stephen Searle
Browse files

insert followed by delete warning message now only printed once.

parent 9c59e7cf
......@@ -476,6 +476,8 @@ sub _parse_cigar {
=cut
my $message_only_once = 1;
sub _parse_features {
my ($self,$features ) = @_;
......@@ -704,8 +706,11 @@ sub _parse_features {
#sanity check, Should not be an insertion and deletion
if($insertion_flag) {
warning("Should not be an deletion and insertion on the " .
"same alignment region. cigar_line=$string\n");
if ($message_only_once) {
warning("Should not be an deletion and insertion on the " .
"same alignment region. cigar_line=$string\n");
$message_only_once = 0;
}
}
}
#shift our position in the hit seq alignment
......@@ -725,9 +730,12 @@ sub _parse_features {
#sanity check, Should not be an insertion and deletion
if($insertion_flag) {
warning("Should not be an deletion and insertion on the " .
"same alignment region. prev2 = $prev2; f->hend() = " .
$f->hend() . "; cigar_line = $string;\n");
if ($message_only_once) {
warning("Should not be an deletion and insertion on the " .
"same alignment region. prev2 = $prev2; f->hend() = " .
$f->hend() . "; cigar_line = $string;\n");
$message_only_once = 0;
}
}
}
#shift our position in the hit seq alignment
......
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