v0.6.9: fix ID matching when no rec.id fixes chapmanb#134

v0.6.8: match records between fasta and GFF with NCBI style headers

NCBI PGAP can produce fastas with NCBI headers (`lcl|1`) and GFFs
with plain IDs (`1`). This avoids creating duplicate records by
matching these and using a consistent contig ID when combining sequences
and GFF files.

The contig ID used in the final output SeqRecords is the first one
encountered. So if you use an external FASTA it's the IDs in the FASTA
and if you use a GFF embedded FASTA it's the IDs in the GFF.

v0.6.7: handle problem sequence-region directives without contigs

Bcbio GFF v0.6.5: Python 3 compatibility; fixes chapmanb#120

Support Biopython 1.68 with sub_features workaround

Biopython deprecated and removed sub_features but the GFF code has not
yet put in proper fixes. This works around the issue by adding
sub_features when missing so GFF output still works correctly
with Biopython >= 1.68.

Fixes chapmanb#110. Fixes biopython/biopython#928

v0.6.2: update version for Python 3 compatibility fixes chapmanb#96

v0.6.1: Provide Python3 compatibility fixes from @TheOneHyer. Also in…

…clude in GFFParser and use six compatibility library for urllib issues. Fixes chapmanb#90

v0.6: Handle trans-splicing GFF cases where child locations may not m…

…atch back to parents. Fixes chapmanb#91

bcbio-gff v0.4

Version 0.6.0 release plus move into own bcbio-nextgen repository