Merge pull request #2017 from Clinical-Genomics/release/11.1.2

release 11.1.2

Author: jemten

CHANGELOG.md

@@ -3,6 +3,10 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [11.1.2]
+
+- Fixed a bug in the mitochondrial deletion recipe affecting samples with 0 intermediate discordant MT reads.
+
 ## [11.1.1]
 
 - Updates chromgraph to version 1.3.1

lib/MIP/Constants.pm

@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{11.1.1};
+Readonly our $MIP_VERSION => q{11.1.2};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

lib/MIP/Recipes/Analysis/Mitodel.pm

@@ -230,14 +230,17 @@ sub analysis_mitodel {
 
     my $awk_statement =
 
+      # Set start value for intermediate discordant
+      q?BEGIN {sum=0} ?
+
       # identification of read pairs that are separated by >1.2 kb but <15 kb
-      q?($2>=1200 && $2<=15000) {sum=sum+$3}?
+      . q?($2>=1200 && $2<=15000) {sum=sum+$3} ?
 
       # identification of normal read pairs which are <1.2 kb but >15 kb
-      . q?($2<1200 || $2>15000) {sum_norm=sum_norm+$3}?
+      . q?($2<1200 || $2>15000) {sum_norm=sum_norm+$3} ?
 
       # Add end rule
-      . q?END?
+      . q?END ?
 
       # ratio of discordant to normal read pairs
       . q?{print "intermediate discordant ", sum, "normal ", sum_norm, "ratio ppk", sum*1000/(sum_norm+sum)}?;

templates/mip_install_config.yaml

@@ -125,7 +125,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:v11.1.1
+    uri: docker.io/clinicalgenomics/mip:v11.1.2
   multiqc:
     executable:
       multiqc: