From fbf680368011b9b4f5bf9d0520ffbdf6896627cc Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Mon, 23 Mar 2020 16:28:21 +0000
Subject: [PATCH 1/5] commit id for preliminary fix to postprocessing

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 8a0d974..596dfdb 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -7,7 +7,7 @@ ENV VER_VCFTOOLS="0.1.16"
 ENV VER_CGPVCF="v2.2.1"
 ENV VER_CAVEMAN="1.14.1"
 ENV VER_BEDTOOLS="2.27.1"
-ENV VER_CGPCAVEPOSTPROC="1.8.9"
+ENV VER_CGPCAVEPOSTPROC="3295d7f5972fe754ff24295bae0fa88ff1307a66"
 ENV VER_CGPCAVEWRAP="1.15.3"
 
 RUN apt-get -yq update

From 2a2dbb0ddf910d9ecb730b1052c35041abae5687 Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Tue, 24 Mar 2020 14:12:33 +0000
Subject: [PATCH 2/5] This appears to fix for when both reads concur, and also
 works for difference when of same qual

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 596dfdb..12f3937 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -7,7 +7,7 @@ ENV VER_VCFTOOLS="0.1.16"
 ENV VER_CGPVCF="v2.2.1"
 ENV VER_CAVEMAN="1.14.1"
 ENV VER_BEDTOOLS="2.27.1"
-ENV VER_CGPCAVEPOSTPROC="3295d7f5972fe754ff24295bae0fa88ff1307a66"
+ENV VER_CGPCAVEPOSTPROC="4604481fb851949a3d74496f36fe6d295227fe3c"
 ENV VER_CGPCAVEWRAP="1.15.3"
 
 RUN apt-get -yq update

From df1492b3d00f8a88e76b0f099f8ae7650bc3ed57 Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Thu, 26 Mar 2020 14:07:07 +0000
Subject: [PATCH 3/5] bump to preformance enhanced version

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 12f3937..dd744dd 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -7,7 +7,7 @@ ENV VER_VCFTOOLS="0.1.16"
 ENV VER_CGPVCF="v2.2.1"
 ENV VER_CAVEMAN="1.14.1"
 ENV VER_BEDTOOLS="2.27.1"
-ENV VER_CGPCAVEPOSTPROC="4604481fb851949a3d74496f36fe6d295227fe3c"
+ENV VER_CGPCAVEPOSTPROC="151d9885b424c2c57d32788ad387302907458b1d"
 ENV VER_CGPCAVEWRAP="1.15.3"
 
 RUN apt-get -yq update

From 679d30eb9a4f890597c36b38ac4d028404575564 Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Mon, 30 Mar 2020 08:48:07 +0000
Subject: [PATCH 4/5] Move to finalised post-proc

---
 Dockerfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index dd744dd..9f690b6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -7,8 +7,7 @@ ENV VER_VCFTOOLS="0.1.16"
 ENV VER_CGPVCF="v2.2.1"
 ENV VER_CAVEMAN="1.14.1"
 ENV VER_BEDTOOLS="2.27.1"
-ENV VER_CGPCAVEPOSTPROC="151d9885b424c2c57d32788ad387302907458b1d"
-ENV VER_CGPCAVEWRAP="1.15.3"
+ENV VER_CGPCAVEPOSTPROC="1.9.0"
 
 RUN apt-get -yq update
 RUN apt-get install -yq --no-install-recommends \

From 1759987ca960daa2b50a58e463e63d2070b71084 Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Mon, 30 Mar 2020 08:55:02 +0000
Subject: [PATCH 5/5] Release items

---
 CHANGES.md                | 8 +++++++-
 Dockerfile                | 2 +-
 lib/Sanger/CGP/Caveman.pm | 2 +-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index 1fb2604..faf5f10 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,11 @@
 # CHANGES
 
+## 1.16.0
+
+* Pulls in cgpCaVEManPostProcessing 1.9.0
+  * Edgecase fix for overlapping reads - cause +1 variant at WGS scale
+  * Major performance improvement (in post processing)
+
 ## 1.15.3
 
 * Build around CaVEMan core [1.14.1](https://github.com/cancerit/CaVEMan/releases/tag/1.14.0)
@@ -24,7 +30,7 @@
 
 ## 1.14.0
 
-* Created Docker file to build a containder for the wrapper. 
+* Created Docker file to build a containder for the wrapper.
 * Added quay.io badge for the image to the README.
 
 ## 1.13.14
diff --git a/Dockerfile b/Dockerfile
index 9f690b6..e391ded 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -42,7 +42,7 @@ FROM ubuntu:16.04
 
 LABEL maintainer="cgphelp@sanger.ac.uk" \
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
-      version="1.15.3" \
+      version="1.16.0" \
       description="cgpCaVEManWrapper docker"
 
 RUN apt-get -yq update
diff --git a/lib/Sanger/CGP/Caveman.pm b/lib/Sanger/CGP/Caveman.pm
index a621e66..9c9b766 100644
--- a/lib/Sanger/CGP/Caveman.pm
+++ b/lib/Sanger/CGP/Caveman.pm
@@ -26,6 +26,6 @@ package Sanger::CGP::Caveman;
 use strict;
 use Const::Fast qw(const);
 
-our $VERSION = '1.15.3';
+our $VERSION = '1.16.0';
 
 1;