From 84011695b2ff2406c16a335106db6831fb67fdfe Mon Sep 17 00:00:00 2001
From: Sunny Cui <scui@illumina.com>
Date: Fri, 3 Dec 2021 16:31:12 -0800
Subject: [PATCH] Update rtgtools to v3.12.1 (#150)

* Update rtgtools to v3.12.1

* update RELEASES.md

* remove empty line

* add .gitattributes

* remove newline
---
 .gitattributes                | 14 ++++++++++++++
 README.md                     |  3 ++-
 RELEASES.md                   |  8 ++++++++
 external/make_dependencies.sh |  7 ++++---
 4 files changed, 28 insertions(+), 4 deletions(-)
 create mode 100644 .gitattributes

diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..9fb85ec
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,14 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto
+
+# Explicitly declare text files you want to always be normalized and converted
+# to native line endings on checkout.
+*.c text
+*.h text
+
+# Declare files that will always have CRLF line endings on checkout.
+*.sln text eol=crlf
+
+# Denote all files that are truly binary and should not be modified.
+*.png binary
+*.jpg binary
\ No newline at end of file
diff --git a/README.md b/README.md
index 3e38411..6188414 100755
--- a/README.md
+++ b/README.md
@@ -429,7 +429,7 @@ can be carried out on a desktop system.
 Hap.py is known to build and run on the following linux distributions (see also the [Dockerfile](Dockerfile)
 for a list of required packages):
 
-    Ubuntu 12.04,14.04,16.04
+    Ubuntu 12.04,14.04,16.04,18.04
     CentOS 5,6,7
 
 Hap.py must be compiled with g++ version 4.9.x or later, or with a recent version of Clang (testing is performed
@@ -481,3 +481,4 @@ export BOOST_ROOT=$HOME/boost_1_55_0_install
 
 The complete list of dependencies / packages to install beforehand can be found
 in the [Dockerfile](Dockerfile).
+
diff --git a/RELEASES.md b/RELEASES.md
index a86c21c..6128106 100755
--- a/RELEASES.md
+++ b/RELEASES.md
@@ -1,4 +1,12 @@
 # Hap.py Release Notes / Change Log
+## v0.3.15
+* Updated rtgtools to v3.12.1
+* Defect remains: https://jira.illumina.com/browse/HAP-373. Use stable som.py v0.3.10.
+
+## v0.3.14
+* Fixed issues created by previous change to convert_gvcf arguments
+* Removed redundant truth and query gvcf parameters in pre.py.
+* som.py no longer hangs; fp.filtered SNV counting is incorrect. https://jira.illumina.com/browse/HAP-373. Use stable som.py v0.3.10.
 
 ## v0.3.12
 
diff --git a/external/make_dependencies.sh b/external/make_dependencies.sh
index fefd3bc..4e0790b 100755
--- a/external/make_dependencies.sh
+++ b/external/make_dependencies.sh
@@ -115,9 +115,9 @@ if [[ ! -z $BUILD_VCFEVAL ]]; then
         cd ${TLD}
         mkdir -p ${TLD}/rtg-tools
         cd rtg-tools
-        wget http://github.com/RealTimeGenomics/rtg-tools/archive/3.10.1.tar.gz -O ${TLD}/rtg-tools/rtg-tools.tar.gz
+        wget http://github.com/RealTimeGenomics/rtg-tools/archive/3.12.1.tar.gz -O ${TLD}/rtg-tools/rtg-tools.tar.gz
         tar xvf rtg-tools.tar.gz
-        cd rtg-tools-3.10.1
+        cd rtg-tools-3.12.1
 
         if [[ ! -z ${ANT_HOME} ]]; then
             $ANT_HOME/bin/ant zip-nojre
@@ -126,7 +126,7 @@ if [[ ! -z $BUILD_VCFEVAL ]]; then
         fi
         cd ..
 
-        RTG_ZIPFILE=$(ls rtg-tools-3.10.1/dist/*-nojre.zip | head -1)
+        RTG_ZIPFILE=$(ls rtg-tools-3.12.1/dist/*-nojre.zip | head -1)
         RTG_BASE=$(basename $RTG_ZIPFILE -nojre.zip)
         jar xvf $RTG_ZIPFILE
         mv $RTG_BASE ${ISD}/libexec/rtg-tools-install
@@ -141,3 +141,4 @@ if [[ ! -z $BUILD_VCFEVAL ]]; then
         chmod +x ${ISD}/libexec/rtg-tools-install/rtg-wrapper.sh
     fi
 fi
+