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bede / kindel

Indel-aware consensus from aligned BAMs
GNU General Public License v3.0
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'mask_ends' is not defined #14

Closed lneaves closed 5 years ago

lneaves commented 5 years ago

When I run Kindel using --realign on the test data. I get the following error. Has something not installed correctly?

kindel consensus --realign -t 6.1.sub_test.bam loading sequences: 16457it [00:01, 14571.11it/s] Traceback (most recent call last): File "/usr/local/bin/kindel", line 11, in sys.exit(main()) File "/home/.local/lib/python3.6/site-packages/kindel/cli.py", line 79, in main parser.dispatch() File "/home/.local/lib/python3.6/site-packages/argh/helpers.py", line 55, in dispatch return dispatch(self, *args, *kwargs) File "/home/.local/lib/python3.6/site-packages/argh/dispatching.py", line 174, in dispatch for line in lines: File "/home/.local/lib/python3.6/site-packages/argh/dispatching.py", line 277, in _execute_command for line in result: File "/home/.local/lib/python3.6/site-packages/argh/dispatching.py", line 260, in _call result = function(positional, **keywords) File "/home/.local/lib/python3.6/site-packages/kindel/cli.py", line 24, in consensus uppercase) File "/home/.local/lib/python3.6/site-packages/kindel/kindel.py", line 377, in bam_to_consensus clip_decay_threshold, mask_ends) NameError: name 'mask_ends' is not defined