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brentp / methylcode

Alignment and Tabulation of BiSulfite Treated Reads
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methylcoder fails when there are spaces in the fasta header names #2

Closed brentp closed 13 years ago

brentp commented 13 years ago

with a fasta header like ">chr1 asdf", pyfasta (used by methylcoder)" will use "chr1 asdf" as the key while bowtie will map using "chr1". this gives a KeyError from pyfasta about not being able to find "chr1". this is bad.

brentp commented 13 years ago

bowtie has an option --fullref, if i just add this to the defaults it will work fine.

brentp commented 13 years ago

fixed as of: https://github.com/brentp/methylcode/commit/30c8881e19dd797f375273f5699b1595db83e1a2