diff --git a/README.md b/README.md index e26fc1f4..67a156ed 100644 --- a/README.md +++ b/README.md @@ -37,16 +37,17 @@ hictk can be installed using containers, bioconda or directly from source. Refer hictk provides the following subcommands: -| subcommand | description | -|----------------|----------------------------------------------------------------------------------------| -| __balance__ | Balance HiC matrices using ICE. | -| __convert__ | Convert matrices between .hic and Cooler formats. | -| __dump__ | Write interactions from .hic or Cooler files to the terminal. | -| __fix-mcool__ | Fix corrupted .mcool files. | -| __load__ | Generate a Cooler file from pixels or pairs of interactions in text format. | -| __merge__ | Merge multiple Cooler files using the same reference assembly. | -| __validate__ | Validate Cooler and .hic files. | -| __zoomify__ | Convert single-resolution cooler files to multi-resolution cooler files by coarsening. | +| subcommand | description | +|------------------------|-------------------------------------------------------------------------------------| +| __balance__ | Balance HiC matrices using ICE. | +| __convert__ | Convert matrices to a different format. | +| __dump__ | Dump data from .hic and Cooler files to stdout. | +| __fix-mcool__ | Fix corrupted .mcool files. | +| __load__ | Build .cool and .hic files from interactions in various text formats. | +| __merge__ | Merge multiple Cooler or .hic files into a single file. | +| __rename-chromosomes__ | Rename chromosomes found in a Cooler file. | +| __validate__ | Validate .hic and Cooler files. | +| __zoomify__ | Convert single-resolution Cooler and .hic files to multi-resolution by coarsening. | Refer to [Quickstart (CLI)](https://hictk.readthedocs.io/en/latest/quickstart_cli.html) and [CLI Reference](https://hictk.readthedocs.io/en/latest/cli_reference.html) for more details. diff --git a/cmake/Versioning.cmake b/cmake/Versioning.cmake index 33e9da39..3d8dc6f2 100644 --- a/cmake/Versioning.cmake +++ b/cmake/Versioning.cmake @@ -4,7 +4,7 @@ set(HICTK_PROJECT_VERSION_MAJOR 0) set(HICTK_PROJECT_VERSION_MINOR 0) -set(HICTK_PROJECT_VERSION_PATCH 6) +set(HICTK_PROJECT_VERSION_PATCH 7) set(HICTK_PROJECT_VERSION_SUFFIX "") option(HICTK_ENABLE_GIT_VERSION_TRACKING "Retrieve project version and metadata from git" ON) diff --git a/docs/cli_reference.rst b/docs/cli_reference.rst index c8698f7c..584a9883 100644 --- a/docs/cli_reference.rst +++ b/docs/cli_reference.rst @@ -27,7 +27,7 @@ Subcommands rename-chromosomes, rename-chroms Rename chromosomes found in a Cooler file. validate Validate .hic and Cooler files. - zoomify Convert single-resolution Cooler file to multi-resolution by coarsening. + zoomify Convert single-resolution Cooler and .hic files to multi-resolution by coarsening. hictk balance ------------- @@ -293,7 +293,7 @@ hictk zoomify .. code-block:: text - Convert single-resolution Cooler file to multi-resolution by coarsening. + Convert single-resolution Cooler and .hic files to multi-resolution by coarsening. Usage: hictk zoomify [OPTIONS] cooler/hic mcool/hic Positionals: cooler/hic TEXT:(Cooler) OR (HiC) REQUIRED diff --git a/docs/conf.py b/docs/conf.py index 7d98a0cb..c68bff97 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -49,7 +49,7 @@ # built documents. # Read the listed version -version = "0.0.6" +version = "0.0.7" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/docs/installation.rst b/docs/installation.rst index 99075a96..ff8df523 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -20,7 +20,7 @@ hictk package for Linux and MacOS is available on bioconda and can be installed hictk: /home/user/.miniconda3/envs/hictk/bin/hictk (hictk) user@dev:/tmp$ hictk --version - hictk-v0.0.6-bioconda + hictk-v0.0.7-bioconda Containers (Docker or Singularity/Apptainer) @@ -66,10 +66,10 @@ Downloading and running the latest stable release can be done as follows: .. code-block:: console # Using Docker, may require sudo - user@dev:/tmp$ docker run ghcr.io/paulsengroup/hictk:0.0.6 --help + user@dev:/tmp$ docker run ghcr.io/paulsengroup/hictk:0.0.7 --help # Using Singularity/Apptainer - user@dev:/tmp$ singularity run ghcr.io/paulsengroup/hictk:0.0.6 --help + user@dev:/tmp$ singularity run ghcr.io/paulsengroup/hictk:0.0.7 --help Blazing fast tools to work with .hic and .cool files. Usage: /usr/local/bin/hictk [OPTIONS] SUBCOMMAND diff --git a/docs/installation_src.rst b/docs/installation_src.rst index 0595c96c..a3cc115f 100644 --- a/docs/installation_src.rst +++ b/docs/installation_src.rst @@ -71,7 +71,7 @@ Using git. git clone https://github.com/paulsengroup/hictk.git /tmp/hictk cd /tmp/hictk - git checkout v0.0.6 # Skip this step if you want to build the latest commit from main + git checkout v0.0.7 # Skip this step if you want to build the latest commit from main Compiling hictk --------------- diff --git a/docs/quickstart_api.rst b/docs/quickstart_api.rst index 10898a00..47d2bc50 100644 --- a/docs/quickstart_api.rst +++ b/docs/quickstart_api.rst @@ -18,7 +18,7 @@ To install libhictk using Conan, first create a conanfile.txt like the following .. code-block:: [requires] - hictk/0.0.6 + hictk/0.0.7 [generators] CMakeDeps @@ -62,7 +62,7 @@ To install and configure hictk using `FetchContent fallthrough() - ->preparse_callback([this]([[maybe_unused]] std::size_t i) { - assert(_config.index() == 0); - _config = ZoomifyConfig{}; - }); + auto& sc = + *_cli.add_subcommand( + "zoomify", + "Convert single-resolution Cooler and .hic files to multi-resolution by coarsening.") + ->fallthrough() + ->preparse_callback([this]([[maybe_unused]] std::size_t i) { + assert(_config.index() == 0); + _config = ZoomifyConfig{}; + }); _config = ZoomifyConfig{}; auto& c = std::get(_config); diff --git a/test/units/bin_table/CMakeLists.txt b/test/units/bin_table/CMakeLists.txt index 36f13d0b..710c7265 100644 --- a/test/units/bin_table/CMakeLists.txt +++ b/test/units/bin_table/CMakeLists.txt @@ -11,10 +11,8 @@ include(Catch) add_executable(bin_table_tests) -target_sources( - bin_table_tests - PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/bin_test.cpp" - "${CMAKE_CURRENT_SOURCE_DIR}/bin_table_test.cpp") +target_sources(bin_table_tests PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/bin_test.cpp" + "${CMAKE_CURRENT_SOURCE_DIR}/bin_table_test.cpp") target_link_libraries( bin_table_tests