Merge branch 'jdaw/release-0.4.1' into 'master'

[release] release v0.4.1

See merge request machine-learning/dorado!648

CHANGELOG.md

@@ -2,6 +2,14 @@
 
 All notable changes to Dorado will be documented in this file.
 
+# [0.4.1] (12 Oct 2023)
+
+This release of Dorado fixes a bug with duplex tags and adds functionality to dorado demux.
+
+* 7fefd5d949d32decc3b347778afa80c90b9c6417 - Fix missing `dx:i:-1` tag for simplex reads with duplex offsprings
+* d532ef1517413b536714d47c01a998305890d922 - Enable dorado debug build in Visual Studio 22
+* eeef7575b6dabab8d5647cebed0f92ef793786ef - Add `dorado demux` option to demux pre-classified barcoded data
+
 # [0.4.0] (9 Oct 2023)
 
 This release of Dorado introduces barcode demultiplexing, barcode trimming, simplex read splitting, and updated models for calling 6mA and 5mC/5hmC modified bases. Furthermore, it contains improvements to duplex pairing for increased yield, basecalling speed enhancements and reductions to memory consumption, bug fixes, and additional tests for enhanced stability.

README.md

@@ -18,10 +18,10 @@ If you encounter any problems building or running Dorado, please [report an issu
 
 ## Installation
 
- - [dorado-0.4.0-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.0-linux-x64.tar.gz)
- - [dorado-0.4.0-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.0-linux-arm64.tar.gz)
- - [dorado-0.4.0-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.0-osx-arm64.zip)
- - [dorado-0.4.0-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.0-win64.zip)
+ - [dorado-0.4.1-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.1-linux-x64.tar.gz)
+ - [dorado-0.4.1-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.1-linux-arm64.tar.gz)
+ - [dorado-0.4.1-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.1-osx-arm64.zip)
+ - [dorado-0.4.1-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.1-win64.zip)
 
 ## Platforms
 
@@ -104,7 +104,9 @@ To run Duplex basecalling, run the command:
 $ dorado duplex [email protected] pod5s/ > duplex.bam
 ```
 
-This command will output both simplex and duplex reads. The `dx` tag in the output BAM can be used to distinguish between them:
+When using the `duplex` command, two types of DNA sequence results will be produced: 'simplex' and 'duplex'. Any specific position in the DNA which is in a duplex read is also seen in two simplex strands (the template and complement).  So, each DNA position which is duplex sequenced will be covered by a minimum of three separate readings in the output.
+
+The `dx` tag in the BAM record for each read can be used to distinguish between simplex and duplex reads:
 * `dx:i:1` for duplex reads.
 * `dx:i:0` for simplex reads which don't have duplex offsprings.
 * `dx:i:-1` for simplex reads which have duplex offsprings.