Tag

Added
- New `NamedIndex` class for storing and retrieving features by ID (see 82).
- New CLI command `tag pep2nuc` for transforming feature coordinates from peptide space to nucleotide space (see 83).

Added
- New `tag.select.merge` function to efficiently merge sorted feature streams (see 68).
- New `tag.locus` module for efficient parsing locus coordinates from multiple annotation streams (see 71).
- New experimental `tag.bae` module for evaluating bacterial annotation (see 73, 76).

Changed
- Minor updates to compensate for a couple years' worth of neglect (see 64).
- Refactored `GFF3Reader` to better support processing of unsorted GFF3 data (see 65).
- Implemented finer control of how and when output separator directives (``) are printed to GFF3 output (see 68, 75).
- Reorganized test suite code and data (see 70).
- Refactored the `Feature` and `Score` APIs with more sane default and static constructors (see 74).

Fixed
- The `GFF3Writer` class now behaves as expected when `.retainids` is set to `True` (see 79).

Fixed
- Missing `extent` query from the index implementation.
- Aliased `index.keys()` to `index.seqids`.

Added
- Script `tag sum` to provide very basic summaries of genomic GFF3 files.

Added
- Pseudo-features for better handling and sorting of top-level multi-features.
- A new `primary_transcript` filter as a generalization of the `primary_mrna`
function.
- A new function to query features for NCBI `GeneID` values.
- A new function to traverse a feature and all of its children to collect all
attribute values associate with a given key.

Fixed
- Bug with non-protein coding genes and the `tag.mrna.primary` filter (now
`primary_mrna` in the `tag.transcript` module).
- Bug with how the GFF3 writer handles multi-feature IDs.

Changed
- Refactored the `mrna` module, extended it, and renamed it to `transcript` to
reflect its new and broader scope.

Fixed
- Range overlap queries accidentally left out of the previous release.

Added
- New convenience functions in the `Range` and `Feature` classes for range and
point overlap queries.