From 9503e6c819593cdb6c82f73472858e992db45003 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Mon, 13 Feb 2023 17:34:37 +0100
Subject: [PATCH] fixing MT deletetion calculation, fixes #2016

---
 CHANGELOG.md                        | 4 ++++
 lib/MIP/Constants.pm                | 2 +-
 lib/MIP/Recipes/Analysis/Mitodel.pm | 9 ++++++---
 templates/mip_install_config.yaml   | 2 +-
 4 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 305ec7aa5..52d1187a8 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
index 71547bd02..8f8c7e6ad 100644
--- a/lib/MIP/Constants.pm
+++ b/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;
diff --git a/lib/MIP/Recipes/Analysis/Mitodel.pm b/lib/MIP/Recipes/Analysis/Mitodel.pm
index 0729f16f3..6f2563f40 100644
--- a/lib/MIP/Recipes/Analysis/Mitodel.pm
+++ b/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)}?;
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index f25b6ddb6..e7dfd3d77 100644
--- a/templates/mip_install_config.yaml
+++ b/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: