Update README.md, CHANGELOG.md, duplex_tools/__init__.py

CHANGELOG.md

@@ -5,6 +5,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## [v0.3.3]
+### Added
+- Deprecation warning. Update sam->bam in readme.
+
 ## [v0.3.2]
 ### Added
 - Update to `dorado_stereo.sh`, do not create directories when using -n flag (dry run).

README.md

@@ -1,5 +1,9 @@
 ![Oxford Nanopore Technologies logo](https://github.com/nanoporetech/medaka/raw/master/images/ONT_logo_590x106.png)
 
+> **Deprecation notice**
+> Please note that the functionality in this repository is superseded by integrated pairing in [Dorado](https://github.com/nanoporetech/dorado/tree/master/dorado).
+> This means it's no longer necessary to use pairing or dorado_stereo.sh in order to perform end-to-end duplex calling. 
+
 # Duplex Tools
 
 Duplex Tools contains a set of utilities for dealing with Duplex sequencing
@@ -58,7 +62,7 @@ For greatest duplex recovery, follow these steps:
 This will create an (unmapped) .sam file which has a mapping between the signal and bases.
 `--emit-moves` allows for additional pairs to be found in step 2b.
 
-    $ dorado basecaller [email protected] pod5s/ --emit-moves > unmapped_reads_with_moves.sam
+    $ dorado basecaller [email protected] pod5s/ --emit-moves > unmapped_reads_with_moves.bam
 
 ### 2a) Find duplex pairs for Dorado stereo/basespace basecalling
 This will detect the majority of pairs and put them in the `pairs_from_bam` directory.

duplex_tools/__init__.py

@@ -10,7 +10,7 @@
     "split_on_adapter", "assess_split_on_adapter",
     "pairs_from_summary", "filter_pairs", "pair", "split_pairs"]
 
-__version__ = '0.3.2'
+__version__ = '0.3.3'
 
 
 def main():