Fix bug where --trim_start and --trim_end were not passed correctly

nanoporetech · Jun 29, 2022 · 3705eeb · 3705eeb
1 parent ebdb5ea
commit 3705eeb
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 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).
 
+## [v0.2.11]
+### Fixed
+- Passed --trim_start and --trim_end from cli to main function for split_on_adapter
+
 ## [v0.2.10]
 ### Added
 - Flags `--trim_start` and `--trim_end` for split_on_adapter (https://github.com/nanoporetech/duplex-tools/issues/13)

diff --git a/duplex_tools/__init__.py b/duplex_tools/__init__.py
@@ -10,7 +10,7 @@
     "split_on_adapter", "assess_split_on_adapter",
     "pairs_from_summary", "filter_pairs"]
 
-__version__ = '0.2.10'
+__version__ = '0.2.11'
 
 
 def main():

diff --git a/duplex_tools/split_on_adapter.py b/duplex_tools/split_on_adapter.py
@@ -362,7 +362,7 @@ def argparser():
         help="How many bases to trim (mask) "
              "from the beginning of the strand" + default)
     parser.add_argument(
-        "--trim_end", default=200, type=int, dest='m',
+        "--trim_end", default=200, type=int,
         help="How many bases to trim (mask) "
              "from the end of the strand" + default)
     return parser
@@ -384,4 +384,7 @@ def main(args):
         args.print_alignment,
         args.print_threshold_delta,
         args.threads,
-        args.allow_multiple_splits)
+        args.allow_multiple_splits,
+        args.trim_start,
+        args.trim_end,
+        )