3.10.0

Author: andrewprzh

VERSION

@@ -1 +1 @@
-3.9.0
+3.10.0

changelog.md

@@ -1,5 +1,12 @@
 # IsoQuant changelog
 
+## IsoQuant 3.10.0, 21 October 2025
+
+- New option `--polya_trimmed` to indicate polyA-trimmed reads (thanks @hmutpw for the suggestion [#342](https://github.com/ablab/IsoQuant/issues/342)).
+- 
+- New option `--process_only_chr` to process a specific list of chromosomes.
+
+
 ## IsoQuant 3.9.0, 1 October 2025
 
 - Secondary alignments are not used by default from now on. It significantly improves running time and RAM consumption, but barely affects the results' quality.

docs/cmd.md

@@ -83,6 +83,7 @@ as having a poly-A tail on the 3' end;
 - `all`: all reads will be considered to be poly-A-trimmed and will be marked as 
 having a poly-A tail on the 3'; read direction will be based on the alignment strand flag. 
 Thus, when using this options, make sure read sequences are properly oriented, i.e. match the original mRNA strand.
+Use this option at your own risk.
 
 `--prefix` or `-p`
     Prefix for all output files and sub-folder name. `OUT` if not set.