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diginorm paired mode #1

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merged 8 commits into from
Jul 17, 2012
Merged

diginorm paired mode #1

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6553fa7
Write FASTQ if the records have quality values
jts Apr 5, 2012
d87f0d9
Implemented --paired mode, which only discards a read pair if both pa…
jts Apr 7, 2012
52de836
Merge from 'ged-lab/master'.
Jul 7, 2012
88831ae
Create tests for Jared's --paired patch. Minor tweaks to the same.
Jul 9, 2012
1b29b9e
Merge pull request #1 from spartanem/jts-master-patched
jts Jul 10, 2012
077583d
In diginorm, only pass paired reads when both pairs and longer than k
jts Jul 10, 2012
9feadc2
Cleaned up logic when discarding short pairs
jts Jul 10, 2012
f034ff9
Comment clarification
jts Jul 10, 2012
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Merge from 'ged-lab/master'.
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Eric McDonald committed Jul 7, 2012
commit 52de8360a62ab106b465829d62c739bcc2a00753
1 change: 1 addition & 0 deletions scripts/normalize-by-median.py
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Expand Up @@ -81,6 +81,7 @@ def main():
output_name = os.path.basename(input_filename) + '.keep'
outfp = open(output_name, 'w')

n = -1
for n, batch in enumerate(batchwise(screed.open(input_filename), batch_size)):
if n > 0 and n % 100000 == 0:
print '... kept', total - discarded, 'of', total, ', or', \
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