Merge pull request #246 from smithlabcode/prep-for-release-v1.4.4

Updates ahead of release v1.4.4
smithlabcode · Oct 20, 2024 · deaff4a · deaff4a
2 parents 8883fd0 + 3cdb089
commit deaff4a
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Showing 6 changed files with 16 additions and 16 deletions.
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@ sequencing (RRBS). These tools focus on overcoming the computing
 challenges imposed by the scale of genome-wide DNA methylation data,
 which is usually the early parts of data analysis.
 
-## Installing release 1.4.3
+## Installing release 1.4.4
 
 The documentation for DNMTools can be found
 [here](https://dnmtools.readthedocs.io). But if you want to install
@@ -42,14 +42,14 @@ repo, it is easiest if all dependencies are available through conda.
 
 ### Configuration
 
-* Download [dnmtools-1.4.3.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.4.3/dnmtools-1.4.3.tar.gz).
+* Download [dnmtools-1.4.4.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.4.4/dnmtools-1.4.4.tar.gz).
 * Unpack the archive:
 ```console
-tar -zxvf dnmtools-1.4.3.tar.gz
+tar -zxvf dnmtools-1.4.4.tar.gz
 ```
 * Move into the dnmtools directory and create a build directory:
 ```console
-cd dnmtools-1.4.3 && mkdir build && cd build
+cd dnmtools-1.4.4 && mkdir build && cd build
 ```
 * Run the configuration script:
 ```console
@@ -139,7 +139,7 @@ docker tag ghcr.io/smithlabcode/dnmtools:latest dnmtools:latest
 
 You can also install the image for a particular vertion by running
 ```console
-docker pull ghcr.io/smithlabcode/dnmtools:v[VERSION NUMBER] #(e.g. v1.4.3)
+docker pull ghcr.io/smithlabcode/dnmtools:v[VERSION NUMBER] #(e.g. v1.4.4)
 ```
 Not all versions have corresponding images; you can find available images
 [here](https://github.com/smithlabcode/dnmtools/pkgs/container/dnmtools).

diff --git a/configure.ac b/configure.ac
@@ -14,7 +14,7 @@ dnl but WITHOUT ANY WARRANTY; without even the implied warranty of
 dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 dnl General Public License for more details.
 
-AC_INIT([dnmtools], [1.4.3], [[email protected]],
+AC_INIT([dnmtools], [1.4.4], [[email protected]],
         [dnmtools], [https://github.com/smithlabcode/dnmtools])
 dnl the config.h is #included in the sources for version info
 AC_CONFIG_HEADERS([config.h])

diff --git a/data/md5sum.txt b/data/md5sum.txt
@@ -17,8 +17,8 @@ ec6a686617cad31e9f7a37a3d378e6ed  tests/two_epialleles.states
 93e38b20d162062a5d147c4290095a13  tests/mlml.out
 d947fe3d61ef7b1564558a69608f0e64  tests/methylome.pmd
 d41d8cd98f00b204e9800998ecf8427e  tests/two_epialleles.amr
-6bbf66748e2a11d5c2736a81efeac270  tests/reads.fmt.sam
-f963e689859dcf38a26acda9a65a6431  tests/reads.sam
-a751b849e0895b2403f8ddd01b647ae1  tests/reads.fmt.srt.uniq.sam
-abb472bdea230af31e0d2b00abb95b02  tests/reads.xcounts
-12e0afdca1387b2805cfee0ea2ddcfea  tests/reads.unxcounts
+fec572ada903add94dda1a01a3da9167  tests/reads.sam
+e74154fedadbc365d8e0a228d6cfa6bb  tests/reads.fmt.sam
+414c2e3aee2c154565f5ee44192ab3a8  tests/reads.fmt.srt.uniq.sam
+c56171d4902381f2ef19cccdfe34f0be  tests/reads.xcounts
+598f2a6ae5d843d6e9acfb611c747b53  tests/reads.unxcounts
diff --git a/docs/content/quickstart.md b/docs/content/quickstart.md
@@ -70,14 +70,14 @@ would need to be activated when you want to use dnmtools.
 
 ### Configuration
 
-* Download [dnmtools-1.4.3.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.4.3/dnmtools-1.4.3.tar.gz).
+* Download [dnmtools-1.4.4.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.4.4/dnmtools-1.4.4.tar.gz).
 * Unpack the archive:
 ```console
-$ tar -zxvf dnmtools-1.4.3.tar.gz
+$ tar -zxvf dnmtools-1.4.4.tar.gz
 ```
 * Move into the dnmtools directory and create a build directory:
 ```console
-$ cd dnmtools-1.4.3
+$ cd dnmtools-1.4.4
 $ mkdir build && cd build
 ```
 * Run the configuration script:

diff --git a/src/abismal b/src/abismal
diff --git a/src/smithlab_cpp b/src/smithlab_cpp
+7 −7		.github/workflows/macos-builds.yml
+6 −6		README.md
+1 −1		configure.ac
+4 −4		data/md5sum.txt
+4 −4		docs/MANUAL.md
+4 −4		docs/abismal.1
+4 −4		docs/abismal.html
+1 −1		src/AbismalIndex.hpp
+2 −0		src/abismal.cpp
+1 −1		src/bamxx
+1 −1		src/smithlab_cpp
+5 −0		.clang-format
+20 −0		.github/workflows/source-format-check.yml
+106 −140		GenomicRegion.cpp
+141 −150		GenomicRegion.hpp
+0 −54		Makefile
+5 −2		Makefile.am
+7 −7		MappedRead.cpp
+2 −4		MappedRead.hpp
+163 −172		OptionParser.cpp
+35 −41		OptionParser.hpp
+9 −10		QualityScore.cpp
+49 −87		QualityScore.hpp
+37 −0		autogen.sh
+3 −4		bisulfite_utils.cpp
+13 −19		bisulfite_utils.hpp
+61 −68		chromosome_utils.cpp
+29 −44		chromosome_utils.hpp
+6 −8		cigar_utils.cpp
+49 −89		cigar_utils.hpp
+1 −0		configure.ac
+2 −0		dna_four_bit.cpp
+22 −32		dna_four_bit.hpp
+7 −13		htslib_wrapper.cpp
+3 −3		htslib_wrapper.hpp
+26 −43		sam_record.cpp
+58 −84		sam_record.hpp
+90 −120		smithlab_os.cpp
+52 −79		smithlab_os.hpp
+49 −47		smithlab_utils.cpp
+247 −209		smithlab_utils.hpp
+5 −10		zlib_wrapper.cpp
+18 −23		zlib_wrapper.hpp