When I used trim command, I face an error as follows:
$ deblur trim -t 200 test.fasta.gz test_trim.fasta.gz
Traceback (most recent call last):
File "INSTALL_DIR/bin/deblur", line 684, in <module>
deblur_cmds()
File "LIBRARY_DIR/click/core.py", line 764, in __call__
return self.main(*args, **kwargs)
File "LIBRARY_DIR/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "LIBRARY_DIR/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "LIBRARY_DIR/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "LIBRARY_DIR/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "INSTALL_DIR/bin/deblur", line 140, in trim
for label, seq in trim_seqs(sequence_generator(seqs_fp), trim_length):
TypeError: trim_seqs() missing 1 required positional argument: 'left_trim_len'
I fixed this problem, adding zero to the function.
Coverage remained the same at 88.911% when pulling ca5a72b4c9bc0c24dd61950a66705853e33c449e on TaskeHAMANO:feature/trim_cmd into 4b4badccdbac8fe9d8f8b3f1349f3700e31b5d7b on biocore:master.
When I used
trim
command, I face an error as follows:I fixed this problem, adding zero to the function.