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bxlab / hifive

Tools for handling HiC and 5C data
MIT License
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a small striping issue #2

Closed sirusb closed 9 years ago

sirusb commented 9 years ago

Hi, First thank you for the great package.

I think there is a small problem in the code when reading RAW format data

in line 194 and 195. https://github.com/bxlab/hifive/blob/819bc8af526c2ab36ec1d44a10a06006e66043c2/hifive/hic_data.py#L194

Shouldn't it be 

 temp[0] = temp[0].strip('chr')
 temp[3] = temp[3].strip('chr')

I tried with a file in the following format 

chr1    10008   +   chr1    10108   -
chr1    10008   +   chr1    234897  -
chr1    12436   +   chr1    12886   -
chr1    12448   +   chr1    12832   -
chr1    12461   +   chr1    12879   -
chr1    12686   +   chr1    62882   +
chr1    12851   +   chr1    13308   -

but I got 0 loaded reads.

Thanks in advance

msauria commented 9 years ago

Thanks for pointing this out. I actually had come across this just the other day and have only now gotten around to pushing a new lease including this fix.

Good catch.