From f196e816d64f5c1297fe5b5e2576f467fa36465e Mon Sep 17 00:00:00 2001 From: Anton Goloborodko <goloborodko.anton@gmail.com> Date: Tue, 23 Apr 2024 17:27:08 +0200 Subject: [PATCH 1/2] update CHANGES.md --- .github/workflows/python-package.yml | 2 +- CHANGES.md | 32 ++++++++++++++++++++++++++++ 2 files changed, 33 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 8e27f0b..c1c10c5 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -16,7 +16,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.7", "3.8", "3.9", "3.10"] + python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"] steps: - uses: actions/checkout@v2 diff --git a/CHANGES.md b/CHANGES.md index b4172ff..5f1f891 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,3 +1,35 @@ +### 1.1.0 (2024-04-23) ### +Major bugfixes: +- Fix a major bug in sort that previously broke the sorting order. This bug was introduced in recent versions of pairtools #230 +- Fix a major bug in dedup that caused pair duplication and broken sorting order in non-Cython backends + +New features: +- stats: calculate the distance of P(s) divergence between pairs of different directionalities #222 +- dedup: allow column names in all backends, and allow sorting by arbitrary columns #162 + +New behavior and default settings: +- dedup: turn mark-dups on by default #211 +- parse: change the default --walks-policy to 5unique +- parse: pair types are now always in upper case. Previously, letters in pair types were converted to lowercase if the corresponding side contained chimeric alignments. + +Minor bugfixes: +- dedup: allow inputs with quotes #194 +- dedup: allow empty input pairs file #201 +- stats: minor bugfixes #200 + +Documentation: +- a new notebook with the statistics of distances between PCR duplicates #233 +- clean up phase walkthrough #218 +- a new chapter on building workflows with pairtools #219 #226 #231 +- a major cleanup + +Code updates: +- make pairsio.py to read (and, in the future, write) .pairs files #195 +- minor refactoring of parse #223 + +New Contributors: +- @hkariti made their first contribution in #194 + ### 1.0.3 (2023-11-20) ### - [x] `pairtools dedup`: update default chunksize to 10,000 to prevent memory overflow on datasets with high duplication rate From 6f7c9223bd1d64e66b392fd75bc9632fd1459c2b Mon Sep 17 00:00:00 2001 From: Anton Goloborodko <goloborodko.anton@gmail.com> Date: Tue, 23 Apr 2024 17:30:15 +0200 Subject: [PATCH 2/2] bump version --- pairtools/__init__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pairtools/__init__.py b/pairtools/__init__.py index c345db1..e5d3e19 100644 --- a/pairtools/__init__.py +++ b/pairtools/__init__.py @@ -4,12 +4,12 @@ CLI tools to process mapped Hi-C data -:copyright: (c) 2017-2023 Open2C +:copyright: (c) 2017-2024 Open2C :author: Open2C :license: MIT """ -__version__ = "1.0.3" +__version__ = "1.1.0" # from . import lib