Misc TODO

[nbokulich]

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 expanded unit tests for assemble.py actions #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