3.6

README.md

@@ -7,7 +7,7 @@
 [![User manual](https://github.com/ablab/IsoQuant/actions/workflows/docs.yml/badge.svg)](https://ablab.github.io/IsoQuant/)
 
 
-# IsoQuant 3.5
+# IsoQuant 3.6
 
 [Full IsoQuant documentation can found here](https://ablab.github.io/IsoQuant/).
 Information in this README is given only for convenience and is not a full user manual.

VERSION

@@ -1 +1 @@
-3.5.2
+3.6.0

changelog.md

@@ -1,16 +1,21 @@
 # IsoQuant changelog
 
+## IsoQuant 3.6.0, 13 September 2024
+
+- Fixed duplicated `noninformative` and `intergenic` reads assignments.
+As a results, fixed duplicated novel transcripts [#236](https://github.com/ablab/IsoQuant/issues/236).
+
 ## IsoQuant 3.5.2, 3 September 2024
 
-- Fix exon counting algorithm [#229](https://github.com/ablab/IsoQuant/issues/229).
+- Fixes exon counting algorithm [#229](https://github.com/ablab/IsoQuant/issues/229).
 
 ## IsoQuant 3.5.1, 26 August 2024
 
-- Fix YAML support in visualization [#222](https://github.com/ablab/IsoQuant/issues/222).
+- Fixed YAML support in visualization [#222](https://github.com/ablab/IsoQuant/issues/222).
 
-- Fix transcript naming when IsoQuant-generated GTF is provided as input [#219](https://github.com/ablab/IsoQuant/issues/219).
+- Fixed transcript naming when IsoQuant-generated GTF is provided as input [#219](https://github.com/ablab/IsoQuant/issues/219).
 
-- Fix `exons` attribute duplication [#219](https://github.com/ablab/IsoQuant/issues/219).
+- Fixed `exons` attribute duplication [#219](https://github.com/ablab/IsoQuant/issues/219).
 
 - Exon ids are now consistent between input and output annotations if present.
 
@@ -21,16 +26,16 @@
 
 - New visualization software developed by [@jackfreeman88](https://github.com/jackfreeman88). See more [here](https://ablab.github.io/IsoQuant/visualization.html).
 
-- Dramatically reduce RAM consumption for grouped counts, about 10-20x decrease on datasets with large number of groups.
+- Dramatically reduced RAM consumption for grouped counts, about 10-20x decrease on datasets with large number of groups.
   Important fix for single-cell data processing. Should fix [#189](https://github.com/ablab/IsoQuant/issues/189).
 
-- Fix [#195](https://github.com/ablab/IsoQuant/issues/195): output GTF contained very similar isoforms and estimated their expression as 0.
+- Fixed [#195](https://github.com/ablab/IsoQuant/issues/195): output GTF contained very similar isoforms and estimated their expression as 0.
 
 - New documentation is now available at [ablab.github.io/IsoQuant](https://ablab.github.io/IsoQuant/).
 
 ## IsoQuant 3.4.2, 13 July 2024
 
-- Dramatically reduce RAM consumption.
+- Dramatically reduced RAM consumption.
 Should fix [#209](https://github.com/ablab/IsoQuant/issues/209).
 
 IsoQuant 3.4.2 was tested on a simulated ONT dataset with 30M reads using 12 threads.
@@ -54,9 +59,9 @@ using custom pickle serialization (when `--high_memory` is used).
 
 ## IsoQuant 3.4.1, 9 May 2024
 
-- Fixes `IndexError: list index out of range` when `--sqanti_output` is set ([#186](https://github.com/ablab/IsoQuant/issues/186)).
+- Fixed `IndexError: list index out of range` when `--sqanti_output` is set ([#186](https://github.com/ablab/IsoQuant/issues/186)).
 
-- Fixes `IndexError: list index out of range` in printing grouped transcript models TPMs ([#187](https://github.com/ablab/IsoQuant/issues/187)).
+- Fixed `IndexError: list index out of range` in printing grouped transcript models TPMs ([#187](https://github.com/ablab/IsoQuant/issues/187)).
 
 - Reduced running time when `--sqanti_output` is set.
 
@@ -174,7 +179,7 @@ and to [@alexandrutomescu](https://github.com/alexandrutomescu) for supporting t
 
 - Fixed duplicate canonical attribute in extended annotation.
 
-- Fix `--resume` option when relative paths were provided.
+- Fixed `--resume` option when relative paths were provided.
 
 ## IsoQuant 3.1.1, 16 January 2023