update to 1.2.5 to fix issue 15

ltnetcase · Sep 7, 2022 · 0c280db · 0c280db
1 parent eb6f0d1
commit 0c280db
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Showing 4 changed files with 9 additions and 6 deletions.
diff --git a/Changes b/Changes
@@ -312,3 +312,6 @@
 
 1.24  Thu Jul  8 13:29:19 2021
     - fix a bug for using csto as the cds length error in stoploss snv mutation annotation, which leads the error extent length.
+
+1.25  Wed 07 Sep 2022 12:09:17 PM CST
+    - fix a bug referenced in issue 15 which influence the multiple aa synonymous variants pDot annotation.
diff --git a/VERSION b/VERSION
@@ -1,2 +1,2 @@
-1.2.4
+1.2.5
 
diff --git a/lib/BedAnno.pm b/lib/BedAnno.pm
@@ -9,13 +9,13 @@ use Time::HiRes qw(gettimeofday tv_interval);
 
 use Tabix;
 
-our $VERSION = '1.24';
+our $VERSION = '1.25';
 
 =head1 NAME
 
 BedAnno - Perl module for annotating variation depend on the BED format database.
 
-=head2 VERSION v1.24
+=head2 VERSION v1.25
 
 From version 0.32 BedAnno will change to support CG's variant shell list
 and use ncbi annotation release 104 as the annotation database
@@ -4506,7 +4506,7 @@ sub getTrChange {
                             $trannoEnt->{p} = 'p.(' . $prRef . $no_parsed_pP . '=)';
                         }
                         else {
-                            $trannoEnt->{p} = 'p.(' . $no_parsed_pP . '_' . ($no_parsed_pP + length($prRef) - 1) . '=)';
+                            $trannoEnt->{p} = 'p.(' . $prBegin . '_' . $no_parsed_pP  . '=)';
                         }
 
                         next;

diff --git a/t/BedAnno.t b/t/BedAnno.t
@@ -3016,8 +3016,8 @@ my $synon_dup_frame = {
     'genepart'       => 'CDS',
     'genepartSO'     => 'SO:0000316',
     'intronIndex'    => '.',
-    'p'              => 'p.(320_321=)',
-    'p3'             => 'p.(320_321=)',
+    'p'              => 'p.(319_320=)',
+    'p3'             => 'p.(319_320=)',
     'postEnd'        => {
         'cDot' => '957',
         'exin' => 'EX2E',