Bump htslib to 1.16 for MM parsing improvements

.gitlab-ci.yml

@@ -72,18 +72,24 @@ deploy-checks:
 
 conda:
     extends: .deploy-conda-linux
+    variables:
+        RECIPEPATH: "../conda"
     before_script:
         - *prep-image
         - export CONDA_PKG=${CI_PROJECT_NAME}
         - export CONDA_PKG_VERSION=${CI_COMMIT_TAG/v/}
-        - cd conda
+        - mkdir conda-build
+        - cd conda-build
 
 conda-mac:
     extends: .deploy-conda-mac
+    variables:
+        RECIPEPATH: "../conda"
     before_script:
         - export CONDA_PKG=${CI_PROJECT_NAME}
         - export CONDA_PKG_VERSION=${CI_COMMIT_TAG/v/}
-        - cd conda
+        - mkdir conda-build
+        - cd conda-build
 
 ### Python
 

CHANGELOG.md

@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.6.3]
+### Changed
+- Bumped htslib version to version 1.16 for fixes to MM tag parsing/validation.
+- Change conda build back to bioconda::htslib since we're using a released version.
+
 ## [v0.6.2]
 ### Fixed
 - Off-by-one in pointless BED field.

conda/build.sh

@@ -2,18 +2,18 @@
 
 NAME=modbam2bed
 
-# self-built htslib
-export HTS_CONF_ARGS="--prefix=${PREFIX} --enable-libcurl --with-libdeflate --enable-plugins --enable-gcs --enable-s3"
-export EXTRA_CFLAGS="-I$PREFIX/include"
-export EXTRA_LDFLAGS="-L$PREFIX/lib"
-export EXTRA_LIBS="-ldl -lhts -ldeflate"
-#export STATIC_HTSLIB=""
-
-## just link to htslib from bioconda
+## self-built htslib
+#export HTS_CONF_ARGS="--prefix=${PREFIX} --enable-libcurl --with-libdeflate --enable-plugins --enable-gcs --enable-s3"
 #export EXTRA_CFLAGS="-I$PREFIX/include"
-#export STATIC_HTSLIB=""
 #export EXTRA_LDFLAGS="-L$PREFIX/lib"
-#export EXTRA_LIBS="-ldl -lhts"
+#export EXTRA_LIBS="-ldl -lhts -ldeflate"
+##export STATIC_HTSLIB=""
+
+# just link to htslib from bioconda
+export EXTRA_CFLAGS="-I$PREFIX/include"
+export STATIC_HTSLIB=""
+export EXTRA_LDFLAGS="-L$PREFIX/lib"
+export EXTRA_LIBS="-ldl -lhts"
 
 OS=$(uname)
 if [[ "$OS" == "Darwin" ]]; then

conda/meta.yaml

@@ -18,21 +18,21 @@ requirements:
         # other things, even when we build our own. When
         # using bioconda htslib the other things can be
         # removed from here
-        - bioconda::htslib>=1.14
-        - libcurl
-        - bzip2
-        - xz
-        - zlib
-        - libdeflate
-        - openssl  # [not osx]
+        - bioconda::htslib>=1.16
+          # - libcurl
+          # - bzip2
+          # - xz
+          # - zlib
+          # - libdeflate
+          # - openssl  # [not osx]
     run:
-        - bioconda::htslib>=1.14
-        - libcurl
-        - bzip2
-        - xz
-        - zlib
-        - libdeflate
-        - openssl  # [not osx]
+        - bioconda::htslib>=1.16
+          # - libcurl
+          # - bzip2
+          # - xz
+          # - zlib
+          # - libdeflate
+          # - openssl  # [not osx]
 
 test:
     commands:

modbampy/__init__.py

@@ -8,7 +8,7 @@
 import libmodbampy
 
 # remember to bump version in src/version.h too
-__version__ = "0.6.2"
+__version__ = "0.6.3"
 ffi = libmodbampy.ffi
 libbam = libmodbampy.lib
 

src/version.h

@@ -1,2 +1,2 @@
 // remember to bump version in modbampy/__init__.py too
-const char *argp_program_version = "0.6.2";
+const char *argp_program_version = "0.6.3";