From d3db8792ea0e89cbfc82e188eb94919526eabbd2 Mon Sep 17 00:00:00 2001 From: Qiyun Zhu Date: Thu, 7 Mar 2024 15:38:50 -0700 Subject: [PATCH] testing changelog links --- CHANGELOG.md | 78 ++++++++++++++++++++++++++-------------------------- 1 file changed, 39 insertions(+), 39 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 072b671..7ecc49d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,14 +3,14 @@ ## Version 0.1.6 (2/22/2024) ### Changed -- Improved performance moderately (#192). -- Parameter `--chunk` is now the number of unique query sequences instead of the number of lines (#192). +- Improved performance moderately ([#192](https://github.com/qiyunzhu/woltka/pull/192)). +- Parameter `--chunk` is now the number of unique query sequences instead of the number of lines ([#192](https://github.com/qiyunzhu/woltka/pull/192)). - Updated GitHub Actions workflow. ### Added -- Added parameter `-x|--exclude`, which will exclude query sequences that are mapped to given reference sequences (such as host genome, spike-in, vector, etc.) (#192). -- Added support for interleaved paired-end SAM files (#191). -- Added native support for PAF file format (#182). +- Added parameter `-x|--exclude`, which will exclude query sequences that are mapped to given reference sequences (such as host genome, spike-in, vector, etc.) ([#192](https://github.com/qiyunzhu/woltka/pull/192)). +- Added support for interleaved paired-end SAM files ([#191](https://github.com/qiyunzhu/woltka/pull/191)). +- Added native support for PAF file format ([#182](https://github.com/qiyunzhu/woltka/pull/182)). ### Fixed - Updated hyperlinks in documentation. @@ -19,70 +19,70 @@ ## Version 0.1.5 (12/25/2022) ### Changed -- Modified the command-line interface. Sub-commands under the `tools` menu were raised to the main menu. For example, `woltka tools collapse` now becomes `woltka collapse` (#176). The `tools` menus is still kept for backward compatibility (#177). -- Improved efficiency of handling BIOM tables (#171, #175). This significantly reduced the memory consumption and runtime of the `collapse` command. -- The `--trim-sub` parameter now takes underscore (`_`) as the default separator, if not explicitly specified (#173). -- Updated installation protocol. Now Woltka can be Conda-installed without explicit pre-installation of biom-format (#174). +- Modified the command-line interface. Sub-commands under the `tools` menu were raised to the main menu. For example, `woltka tools collapse` now becomes `woltka collapse` ([#176](https://github.com/qiyunzhu/woltka/pull/176)). The `tools` menus is still kept for backward compatibility ([#177](https://github.com/qiyunzhu/woltka/pull/177)). +- Improved efficiency of handling BIOM tables ([#171](https://github.com/qiyunzhu/woltka/pull/171), [#175](https://github.com/qiyunzhu/woltka/pull/175)). This significantly reduced the memory consumption and runtime of the `collapse` command. +- The `--trim-sub` parameter now takes underscore (`_`) as the default separator, if not explicitly specified ([#173](https://github.com/qiyunzhu/woltka/pull/173)). +- Updated installation protocol. Now Woltka can be Conda-installed without explicit pre-installation of biom-format ([#174](https://github.com/qiyunzhu/woltka/pull/174)). ### Added -- Upgraded the `collapse` command. Now it can collapse using internal hierarchies of feature IDs, such as genome-gene pairs, taxonomic lineages, and EC numbers. This upgrade enables stratified taxonomic/functional analysis of coord-matching ORF tables, without explicitly stratifying them during the classification step (which otherwise is time and space-consuming). The output should be identical to the that of the old method (#173). -- Added a feature to the `normalize` command, which can extract gene lengths from a gene coordinates file. This enables convenient length-based normalization of an existing gene (ORF) profile. For example, it can convert raw frequencies into RPK (#179). +- Upgraded the `collapse` command. Now it can collapse using internal hierarchies of feature IDs, such as genome-gene pairs, taxonomic lineages, and EC numbers. This upgrade enables stratified taxonomic/functional analysis of coord-matching ORF tables, without explicitly stratifying them during the classification step (which otherwise is time and space-consuming). The output should be identical to the that of the old method ([#173](https://github.com/qiyunzhu/woltka/pull/173)). +- Added a feature to the `normalize` command, which can extract gene lengths from a gene coordinates file. This enables convenient length-based normalization of an existing gene (ORF) profile. For example, it can convert raw frequencies into RPK ([#179](https://github.com/qiyunzhu/woltka/pull/179)). - Extended description of stratification and collapsing protocols in the documentation. ### Fixed -- Fixed a bug in parsing sample ID lists (#164). +- Fixed a bug in parsing sample ID lists ([#164](https://github.com/qiyunzhu/woltka/pull/164)). ## Version 0.1.4 (04/27/2022) ### Changed -- Used a single integer to store gene and read information in the ordinal mapper; use bitwise operations to parse the information. This significantly reduced memory consumption (#142). -- Improved alignment file processing efficiency (#153). -- Updated installation protocol. Currently a single `pip install` command should suffice (#145). -- Updated GitHub Actions test from Python 3.6 to Python 3.8. The program itself should continue to support Python 3.6+ (#158). +- Used a single integer to store gene and read information in the ordinal mapper; use bitwise operations to parse the information. This significantly reduced memory consumption ([#142](https://github.com/qiyunzhu/woltka/pull/142)). +- Improved alignment file processing efficiency ([#153](https://github.com/qiyunzhu/woltka/pull/153)). +- Updated installation protocol. Currently a single `pip install` command should suffice ([#145](https://github.com/qiyunzhu/woltka/pull/145)). +- Updated GitHub Actions test from Python 3.6 to Python 3.8. The program itself should continue to support Python 3.6+ ([#158](https://github.com/qiyunzhu/woltka/pull/158)). ### Added -- Added a naive algorithm for read-gene matching when the number of reads is small. This improves speed (#148). -- Added support for stdin as input. This lets the program take a variety of previously unsupported alignment formats (#155). -- Added or updated several pieces of documentation, such as a RefSeq tutorial (#157). -- Experimentally added a much accelerated ordinal mapper, powered by NumPy and Numba (branch `numba`) (#152). +- Added a naive algorithm for read-gene matching when the number of reads is small. This improves speed ([#148](https://github.com/qiyunzhu/woltka/pull/148)). +- Added support for stdin as input. This lets the program take a variety of previously unsupported alignment formats ([#155](https://github.com/qiyunzhu/woltka/pull/155)). +- Added or updated several pieces of documentation, such as a RefSeq tutorial ([#157](https://github.com/qiyunzhu/woltka/pull/157)). +- Experimentally added a much accelerated ordinal mapper, powered by NumPy and Numba (branch `numba`) ([#152](https://github.com/qiyunzhu/woltka/pull/152)). ## Version 0.1.3 (08/27/2021) ### Changed -- Migrated from Travis CI to GitHub Actions (#127). -- Made `--map-as-rank` default when only mapping file(s) are provided (#132). -- Renamed `--normalize|-z` as `--frac|-f` (#128). -- Modified core algorithm which slightly improved performance (#124). +- Migrated from Travis CI to GitHub Actions ([#127](https://github.com/qiyunzhu/woltka/pull/127)). +- Made `--map-as-rank` default when only mapping file(s) are provided ([#132](https://github.com/qiyunzhu/woltka/pull/132)). +- Renamed `--normalize|-z` as `--frac|-f` ([#128](https://github.com/qiyunzhu/woltka/pull/128)). +- Modified core algorithm which slightly improved performance ([#124](https://github.com/qiyunzhu/woltka/pull/124)). ### Added -- Added `tool normalize` command, with multiple features (#124). -- Added the feature to collapse a stratified table (#126). -- Created an WoL FTP server, and added link to it (#118). -- Added an WoL standard operating procedure (`wolsop.sh`) and documentation (#116). -- Added first [citation](https://www.biorxiv.org/content/10.1101/2021.04.04.438427v1.abstract) of Woltka (#111). -- Added protocols for Bowtie2 / SHOGUN and Fastp (#121). -- Added discussion about mapping uniqueness (#131). +- Added `tool normalize` command, with multiple features ([#124](https://github.com/qiyunzhu/woltka/pull/124)). +- Added the feature to collapse a stratified table ([#126](https://github.com/qiyunzhu/woltka/pull/126)). +- Created an WoL FTP server, and added link to it ([#118](https://github.com/qiyunzhu/woltka/pull/118)). +- Added an WoL standard operating procedure (`wolsop.sh`) and documentation ([#116](https://github.com/qiyunzhu/woltka/pull/116)). +- Added first [citation](https://www.biorxiv.org/content/10.1101/2021.04.04.438427v1.abstract) of Woltka ([#111](https://github.com/qiyunzhu/woltka/pull/111)). +- Added protocols for Bowtie2 / SHOGUN and Fastp ([#121](https://github.com/qiyunzhu/woltka/pull/121)). +- Added discussion about mapping uniqueness ([#131](https://github.com/qiyunzhu/woltka/pull/131)). ### Fixed -- Fixed free-rank classification subject not found issue (#120). -- Corrected paths to example files and directories (#117). +- Fixed free-rank classification subject not found issue ([#120](https://github.com/qiyunzhu/woltka/pull/120)). +- Corrected paths to example files and directories ([#117](https://github.com/qiyunzhu/woltka/pull/117)). ## Version 0.1.2 (03/31/2021) ### Changed -- Updated Qiita documentation (#107). -- Renamed "gOTU" with "OGU" (#104). +- Updated Qiita documentation ([#107](https://github.com/qiyunzhu/woltka/pull/107)). +- Renamed "gOTU" with "OGU" ([#104](https://github.com/qiyunzhu/woltka/pull/104)). ### Added -- Published at PyPI. Can be installed by `pip install woltka` (#108). -- Added instructions for using MetaCyc and KEGG (#99, #101). -- Added `tool collapse` command, which supports one-to-many classification (#99). +- Published at PyPI. Can be installed by `pip install woltka` ([#108](https://github.com/qiyunzhu/woltka/pull/108)). +- Added instructions for using MetaCyc and KEGG ([#99](https://github.com/qiyunzhu/woltka/pull/99), [#101](https://github.com/qiyunzhu/woltka/pull/101)). +- Added `tool collapse` command, which supports one-to-many classification ([#99](https://github.com/qiyunzhu/woltka/pull/99)). ### Fixed -- Fixed Handling of zero length alignment (#105). +- Fixed Handling of zero length alignment ([#105](https://github.com/qiyunzhu/woltka/pull/105)). ## Version 0.1.1 (02/17/2021)