Merge pull request #15 from eastgenomics/remove_flanks

remove 5 bp flank addition
eastgenomics · May 20, 2020 · 79b620a · 79b620a
2 parents 2915b40 + f75ca0f
commit 79b620a
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/resources/home/dnanexus/vcf2xls_nirvana.pl b/resources/home/dnanexus/vcf2xls_nirvana.pl
@@ -962,7 +962,7 @@ sub gene_performance {
     $worst_exon{ "$RefSeq" }{'1to5'}    += range2length($$coverage{'1to5'});
     $worst_exon{ "$RefSeq" }{'6to9'}    += range2length($$coverage{'6to9'});
     $worst_exon{ "$RefSeq" }{'10to19'}  += range2length($$coverage{'10to19'});
-    $worst_exon{ "$RefSeq" }{'transcript_length'}  += $$region{ 'end' }-$$region{ 'start' } + 1 + 10; # 5bp flank * 2 = 10
+    $worst_exon{ "$RefSeq" }{'transcript_length'}  += $$region{ 'end' }-$$region{ 'start' } + 1; # 0 vs 1 based coordinates
 
     $exons{ "$RefSeq" }{ $exon_name }{ 'coverage' } = $coverage;
     $exons{ "$RefSeq" }{ $exon_name }{ "$RefSeq" }{ 'region' }   = $region;