Typesafe Coordinates and Reference Counting

This release involves breaking changes to the D API: Typesafe Coordinates (manuscript forthcoming; see https://github.com/blachlylab/typesafe-coordinates) are used throughout the entire interface to eliminate off-by-one errors.

New features since 0.12.0:

• Support htslib 1.13, 1.12, and 1.11 (including all new functions available through 1.13)
• Moved all wrapper structs (SAM/VCFFile; SAM/VCFReader/Writer, CIGAR, TagValue, etc.) to reference counted with automatic memory cleanup when out of scope
  • This uses new HtslibMemory wrapper struct with transparent pointer aliasing if you are feeling dangerous
• Typesafe Coordinates (https://github.com/blachlylab/typesafe-coordates/)
• Typesafe Coordinates is a subpackage, so you can use dhtslib:coordinates without needing htslib!
• The entire D side of the package (i.e. all high level interfaces, but not not the C bindings) take and/or receive typesafe coordinates.
• Integration of the GFF3D (https://github.com/blachlylab/gff3d) GFF3 reader package; add writer
• BED reader/writer (again, you guessed it, using typesafe coordinates)
• Remove GC allocation from coloration of log messages
• Markedly improved test coverage
• VCF: INFO and FORMAT field getters and setters, along with structs to represent and convert those data
• Support -dip1000 compilation
• Marked many D side functions as one or more of @safe @nogc nothrow pure
• Marked the most of C htslib bindings as @nogc nothrow ; some also @system
• Made some ranges (like BAM RecordRange) a forward range for better Phobos range API compat
• FASTA faidx opDollar (i.e., fai["chrom1", 1 .. $]) indexing

Bugfixes

• Many and sundry
• Tabix bugfixes
• Random buffer overflows
• Rare early-deallocation errors with reference counted wrapper structs

What's Changed

• Initial support for SAMReader["chrWHATEVA", x .. $] by @jblachly in #50
• changes to qscore functions by @charlesgregory in #53
• Cigar and md changes by @charlesgregory in #58
• Bgzf reader by @charlesgregory in #28
• htslib 1.12 compatibility by @charlesgregory in #79
• CoordinateSystem Implementation and Adoption by @charlesgregory in #71
• Other file formats by @charlesgregory in #80
• Fix typo in readme by @thewilsonator in #83
• apt-get update github actions by @jblachly in #87
• Remove GC allocation from coloration of log messages by @thewilsonator in #84
• htslib 1.13 compatibility by @charlesgregory in #90
• Coordinate system improvements by @charlesgregory in #88
• VCF Overhaul by @charlesgregory in #105
• Htslib package changes by @charlesgregory in #109
• Coordinate subpackage by @charlesgregory in #111
• Reference Counting fixes and consolidation by @charlesgregory in #108
• Release v0.13.3+htslib-1.13 by @charlesgregory in #113

New Contributors

• @thewilsonator made their first contribution in #83

Full Changelog: v0.10.3...v0.13.3+htslib-1.13