biocore / deblur

Deblur is a greedy deconvolution algorithm based on known read error profiles.
BSD 3-Clause "New" or "Revised" License
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[BUG] Bug fix to use trim command #192

Open suzuki-shm opened 5 years ago

suzuki-shm commented 5 years ago

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.

coveralls commented 5 years ago

Coverage Status

Coverage remained the same at 88.911% when pulling ca5a72b4c9bc0c24dd61950a66705853e33c449e on TaskeHAMANO:feature/trim_cmd into 4b4badccdbac8fe9d8f8b3f1349f3700e31b5d7b on biocore:master.