update various docs

open2c · Feb 23, 2021 · 254695a · 254695a
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -25,4 +25,4 @@
 UNMAPPED_POS = 0
 UNMAPPED_STRAND = '-'
 
-UNANNOTATED_RFRAG = -1
+UNANNOTATED_RFRAG = -1