Ideas for the next major release

[daler]

Integration with other packages

If pybedtools.pkg_integration = True, then:

1. Iterating over SAM or BAM yields pysam.AlignedRead objects
2. Iterating over VCF yields cyvcf2.Variant objects
3. (?) Iterating over GTF/GTF yields gffutils.Feature objects

Simplified iteration

The IntervalIterator in Cython has historically been problematic. It would be cleaner to re-implement in Python, especially if we're aiming for integration with other packages.

• Can we reimplement IntervalIterator in pure Python?
• How much speed does the cbedtool.pyx Cython module gain us in everyday usage?
• How do we weigh any speed gains against maintenance burden?
• If we re-implement Interval objects in Python, what is the bottleneck:
  • when iterating over a BedTool object
  • when sending Intervals to stdin

Evaluate MIT license

• Change in license of bedtools #286