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fastaq: ValueError: empty range for randrange() (191,191, 0) #75

@mmokrejs

Description

@mmokrejs

Hi,
it seems fastaq breaks on some lines. Second, could there be an option to keep the remainder sequence, instead of discarding it?

...
Warning, sequence  1632257 191 25609  too short.  Skipping it...
Warning, sequence  1632262 318 5425  too short.  Skipping it...
Warning, sequence  1632263 187 200  too short.  Skipping it...
Warning, sequence  1632264 282 990  too short.  Skipping it...
Warning, sequence  1632268 319 3229  too short.  Skipping it...
Warning, sequence  1632275 326 2232  too short.  Skipping it...
Warning, sequence  1632278 319 2078  too short.  Skipping it...
Warning, sequence  1632279 311 1726  too short.  Skipping it...
Traceback (most recent call last):
  File "/usr/lib/python-exec/python3.5/fastaq", line 71, in <module>
    exec('pyfastaq.runners.' + task + '.run("' + tasks[task] + '")')
  File "<string>", line 1, in <module>
  File "/usr/lib64/python3.5/site-packages/pyfastaq/runners/to_perfect_reads.py", line 51, in run
    middle_pos = random.randint(ceil(0.5 *isize), floor(len(ref) - 0.5 * isize))
  File "/usr/lib64/python3.5/random.py", line 227, in randint
    return self.randrange(a, b+1)
  File "/usr/lib64/python3.5/random.py", line 205, in randrange
    raise ValueError("empty range for randrange() (%d,%d, %d)" % (istart, istop, width))
ValueError: empty range for randrange() (191,191, 0)
$ fastaq version
3.17.0
$

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