From cd9ab8bc2ea0b020cf364be19788dc9211b5b5fc Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Thu, 5 Feb 2004 18:27:16 +0000
Subject: [PATCH] add more classes of mapping failure
---
misc-scripts/chimp/ErrCode.pm | 35 +++++++++++++++++++++++++++--------
1 file changed, 27 insertions(+), 8 deletions(-)
diff --git a/misc-scripts/chimp/ErrCode.pm b/misc-scripts/chimp/ErrCode.pm
index af22e3ce07..af0067587f 100644
--- a/misc-scripts/chimp/ErrCode.pm
+++ b/misc-scripts/chimp/ErrCode.pm
@@ -9,7 +9,7 @@ use vars qw(@EXPORT_OK @ISA);
@ISA = qw(Exporter);
-@EXPORT_OK = qw(&set_err &get_err &ec2str);
+@EXPORT_OK = qw(&push_err &pop_err &ec2str);
use constant OK => 0;
@@ -34,17 +34,27 @@ use constant TRANSCRIPT_SCAFFOLD_SPAN => 22;
use constant TRANSCRIPT_DOES_NOT_TRANSLATE => 30;
+use constant PART_EXON_CDS_DELETE_FIVE_PRIME_TOO_LONG => 40;
+use constant PART_EXON_CDS_DELETE_THREE_PRIME_TOO_LONG => 41;
+use constant PART_EXON_CDS_DELETE_MIDDLE_TOO_LONG => 42;
-my $ERR;
-sub set_err {
- $ERR = shift;
+my @ERR_STACK = ();
+
+sub push_err {
+ my $err = shift || return;
+ my $err_desc = shift || '';
+
+ push @ERR_STACK, [$err, $err_desc];
}
-sub get_err {
- my $cur_err = $ERR;
- $ERR = OK;
- return $cur_err;
+sub pop_err {
+ my ($err, $err_desc);
+
+ return () if(!@ERR_STACK);
+
+ my $arref = pop(@ERR_STACK);
+ return @$arref;
}
@@ -100,6 +110,15 @@ sub ec2str {
elsif($ec == TRANSCRIPT_SCAFFOLD_SPAN) {
$str = 'Transcript spans multiple scaffolds.';
}
+ elsif($ec == PART_EXON_CDS_DELETE_FIVE_PRIME_TOO_LONG) {
+ $str = "CDS deletion at 5' end of exon too long.";
+ }
+ elsif($ec == PART_EXON_CDS_DELETE_THREE_PRIME_TOO_LONG) {
+ $str = "CDS deletion at 3' end of exon too long.";
+ }
+ elsif($ec == PART_EXON_CDS_DELETE_MIDDLE_TOO_LONG) {
+ $str = "CDS deletion in middle of exon too long.";
+ }
return $str;
}
--
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