Regression in version 0.21.0 (installed via PyPI)
When converting a small mpileup file to wiggle using version 0.21.0, I stumbled on the following error:
Traceback (most recent call last):
File "/home/bow/devel/sandbox/.virtualenvs/bio/bin/piletools", line 9, in <module>
load_entry_point('piletools==0.21.0', 'console_scripts', 'piletools')()
File "/home/bow/devel/sandbox/.virtualenvs/bio/lib/python2.7/site-packages/piletools/piletools.py", line 239, in main
name, name)
File "/home/bow/devel/sandbox/.virtualenvs/bio/lib/python2.7/site-packages/wiggelen/wiggle.py", line 326, in write
for region, position, value in walker:
File "/home/bow/devel/sandbox/.virtualenvs/bio/lib/python2.7/site-packages/piletools/piletools.py", line 172, in mpileup2wig
for record in PileReader(handle):
File "/home/bow/devel/sandbox/.virtualenvs/bio/lib/python2.7/site-packages/piletools/piletools.py", line 120, in next
return PileRecord(line)
File "/home/bow/devel/sandbox/.virtualenvs/bio/lib/python2.7/site-packages/piletools/piletools.py", line 62, in __init__
for variant in BaseReader(self.ref, self.bases, self.qual):
File "/home/bow/devel/sandbox/.virtualenvs/bio/lib/python2.7/site-packages/piletools/basereader.py", line 103, in next
self.qualities[self.qual_offset])])
IndexError: string index out of range
The command I used was:
piletools mpileup2wig -g tech_01.mpileup tech_01.wig
I saw no errors when using version 0.21.0-dev (which I had to explicitly install with pip install piletools==0.21.0-dev
).
The tech_01.mpileup
file (uploaded here) seems fine, so this seems to be due to something between 0.21.0-dev
and 0.21.0
Thanks before for checking :).