diff --git a/CHANGES.md b/CHANGES.md index 8084596f..5ce28118 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,6 +1,16 @@ -### 0.3.0 agalitsyna fork (2020-02-04) ### - -* One-Read-Based Interactions Annotation (ORBITA) option added +### 0.3.1 (2021-02-XX) ### + +* sample: a new tool to select a random subset of pairs +* parse: add --readid-transform to edit readID +* parse: add experimental --walk-policy all (note: it will be moved + to a separate tool in future!) +* all tools: use bgzip if pbgzip not available + +Internal changes: +* parse: move most code to a separate _parse module +* _headerops: add extract_chromosomes(header) +* all tools: drop py3.5 support +* switch from travis CI to github actions ### 0.3.0 (2019-04-23) ### diff --git a/LICENSE b/LICENSE index b0e4f2a4..3d0c03a3 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2017-2020 Open2C +Copyright (c) 2017-2021 Open2C Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 43165ff3..e5d5a276 100644 --- a/README.md +++ b/README.md @@ -5,9 +5,6 @@ [![Join the chat at https://gitter.im/mirnylab/distiller](https://badges.gitter.im/mirnylab/distiller.svg)](https://gitter.im/mirnylab/distiller?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1490831.svg)](https://doi.org/10.5281/zenodo.1490831) -This is a fork of pairtools of mirnylab adapted for -One-Read-Based Interactions Annotation (ORBITA). - ## Process Hi-C pairs with pairtools `pairtools` is a simple and fast command-line framework to process sequencing diff --git a/doc/conf.py b/doc/conf.py index 062d300f..e1e1eb2c 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -48,7 +48,7 @@ # General information about the project. project = 'pairtools' -copyright = '2017-2020, Open2C' +copyright = '2017-2021, Open2C' author = 'Open2C' # The version info for the project you're documenting, acts as replacement for diff --git a/pairtools/__init__.py b/pairtools/__init__.py index 60650c91..2528d94c 100644 --- a/pairtools/__init__.py +++ b/pairtools/__init__.py @@ -5,7 +5,7 @@ CLI tools to process mapped Hi-C data -:copyright: (c) 2017-2020 Open2C +:copyright: (c) 2017-2021 Open2C :author: Open2C :license: MIT diff --git a/pairtools/_pairsam_format.py b/pairtools/_pairsam_format.py index b083b4e4..84963854 100644 --- a/pairtools/_pairsam_format.py +++ b/pairtools/_pairsam_format.py @@ -25,4 +25,4 @@ UNMAPPED_POS = 0 UNMAPPED_STRAND = '-' -UNANNOTATED_RFRAG = -1 \ No newline at end of file +UNANNOTATED_RFRAG = -1