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License: BSD 3-Clause "New" or "Revised" License
Phylogenomics toolkit and pipelines
License: BSD 3-Clause "New" or "Revised" License
Running list of miscellaneous to-do items (current list is from review of #7, edit or add new comment for additional items)
make dict of default params for each method
remove commented-out code blocks
add single-end mode for map reads etc
dereplicate redundant code between map_reads and filter
add unit tests for all _assemble.py methods (see #12)
revisit feature table construction method in consensus_sequence
add validation for PileUpTSVFormat, GenBankFormat
move Bowtie2IndexDirFmt -> DNAFASTAFormat transformer to q2-types
add support for GenBank format (see note in plugin_setup.py)
ceil_coefficient description could be clearer; maybe specify that this is the max number of non-ACGT characters as a fraction of read length.
ceil_coefficient should have a range specified
refactor test_assemble.py code to reduce duplication where possible (e.g., the consensus sequence tests)
determine if it makes sense to allow overlapping sample ids in the consensus sequence step (i.e., one sample giving rise to multiple different genomes) - currently this is explicitly disallowed
Type for some actions should be: SampleData[AlignmentMap % Sorted]
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