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 +