Major changes to filter_reads #141
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* Renamed to subset_reads which more closely reflects its actual function * Now ignores taxonomic assignments not passing filter * Added --include-lowconf which allows users to include taxonomic assignments not passing filter * Modified test TSV to make some taxonomic assignments fail filter * Recalculated test files and hashes manually
* Switch from FASTXIterator to skbio.io (slow) * Passing --no-validate only verifies reads begin with '@' * Restructure iterators to reduce statements in innermost loop * Add support for bzip'd FASTX files * Catch mismatch of TSV and FASTX file lengths
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| (False, False, True, False), # --with-children | ||
| (False, False, True, False), # --exclude-reads | ||
| (False, False, True, True), # --with-children --exclude-reads | ||
| (False, False, False, False, False), |
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This is insane, but OK 😱
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It's just well-tested.
onecodex/scripts/subset_reads.py
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| @click.option('--split-pairs', default=False, is_flag=True, | ||
| help='By default, if either read in a pair matches, both will match. Choose this ' | ||
| 'option to consider each paired-end read separately. Resulting files may *not* ' | ||
| 'have the same number of reads!') |
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Let's call it --subset-pairs-independently and have the following help message:
By default, if either read in a pair matches, both will be retained in the subset file. With this option, R1 and R2 files will be evaluated independently. Note that the subset output FASTQs are *not* guaranteed to have the same number of reads!
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Changed as requested.
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This pull request addresses #79 by:
In addition, this PR might break existing code by: