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Make refactor #164

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wants to merge 27 commits into from
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Make refactor #164

wants to merge 27 commits into from

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averagehat
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see discussion in #156 #155 #152
The current plan is to use jinja templating

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I was wrong about bwa or samtools being able to tag reads intelligently; they can only do it on a per-file basis if you pass that info along with the bwa mem call.

Is there good reason not to map each unpaired fastq file separately and compile them after the mapping?

sangers = filter(is_sanger, files)
def convert_file(fn):
reads = list(SeqIO.parse(fn, 'fastq'))
os.remove(fn)
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If an exception is raised in this block you will lose the file

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no one wanted you :(

@averagehat averagehat closed this Feb 25, 2016
@necrolyte2 necrolyte2 deleted the make-refactor branch March 3, 2016 13:42
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