diff --git a/CHANGES.md b/CHANGES.md index b5e2ef94..b82bfa86 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,45 +1,32 @@ -### 0.4.0 (2022-06-XX) ### +### 1.0.0 (2022-08-XX) ### -This is a major release +This is a major release of pairtools since last release (April 2019!) -* parse -- [x] parse complex walks engine and tools: https://github.com/open2c/pairtools/pull/109 -- [x] stdin and stdout reporting defaults: https://github.com/open2c/pairtools/issues/48 -- [x] flipping issue: https://github.com/open2c/pairtools/issues/91 +#### Post merge: -Reporting: -- pair types [] -- new fields -- report all +- [x] sphinx docs update with incorporated walkthroughs -- changes in defaults +#### New tools: +- [x] parse2 module with CLI for parsing complex walks +- [x] scaling and header modules with CLI -* parse2 +#### Fixes by modules: -* pairtools dedup +pairtools dedup - [x] finalize detection of optical duplicates https://github.com/open2c/pairtools/issues/106 and https://github.com/open2c/pairtools/issues/59, also related to https://github.com/open2c/pairtools/issues/54 - [x] chunked dedup by @Phlya - [x] improvement of dedup to include reporting of the parent readID by @Phlya and @agalitsyna -* dedup: implemented in chunks with two new backends ("scipy", "sklearn"). Now allows to - record the readID of the retained "parent" read from a duplicate cluster in an extra - field in the file with duplicates. New backends rely on the header to define column - oder in the file, specification through CLI arguments works for the "cython" backend, - but it will be removed in a future version. - Note that with non-zero max-mismatch the behaviour of the new backends can be - different from the old "cython": now duplication is transitive (i.e. if read A is a - duplicate of read B, and read B - of read C, reads A and C are now considered - duplicates). - -Note: this is the header post connecting multiple issues, feel free to update and improve! - - pairtools stats/scaling - [x] split dedup stats and regular stats - [x] output chromosome size to the stats output https://github.com/open2c/pairtools/issues/83 - [x] pairtools stats: YAML output? https://github.com/open2c/pairtools/issues/111 and https://github.com/open2c/pairtools/issues/79 - [x] pairtools scaling tool which takes into account chromosome sizes: https://github.com/open2c/pairtools/issues/81, https://github.com/open2c/pairtools/issues/56? +pairtools parse +- [x] parse complex walks engine and tools: https://github.com/open2c/pairtools/pull/109 +- [x] stdin and stdout reporting defaults: https://github.com/open2c/pairtools/issues/48 +- [x] flipping issue: https://github.com/open2c/pairtools/issues/91 pairtools phase - [x] make work with both pip and github versions of bwa: https://github.com/open2c/pairtools/pull/114 @@ -66,14 +53,12 @@ Code maintenance - [x] Clean up deprecation warnings, e.g. https://github.com/open2c/pairtools/issues/71 - [x] Fix input errors without explanations, e.g. https://github.com/open2c/pairtools/issues/61 -#### Specific proposals: +#### Specific changes: Docs improvements - [x] pairtools walkthrough - [x] phasing walkthrough - [x] parse docs update -- [x] sphinx docs update with incorporated walkthroughs - Tests proposals - [x] add tests for dedup @Phlya : https://github.com/open2c/pairtools/issues/5 @@ -83,7 +68,8 @@ Enhancements - [x] add summaries: https://github.com/open2c/pairtools/pull/105 - [x] support of [bwa mem2]( https://github.com/bwa-mem2/bwa-mem2), which is 2-3 times faster than usual bwa mem: https://github.com/open2c/pairtools/discussions/118 - [x] I/O single utility instead of repetitive code in each module - + + ### 0.3.1 (2021-02-XX) ### * sample: a new tool to select a random subset of pairs diff --git a/pairtools/__init__.py b/pairtools/__init__.py index e4aa6788..0ca13d69 100644 --- a/pairtools/__init__.py +++ b/pairtools/__init__.py @@ -10,6 +10,6 @@ """ -__version__ = "1.0.0-dev1" +__version__ = "1.0.0" # from . import lib