package bio_io

Unreleased

0.7.0 (2023-09-10)

• Update Jane Street libraries to v0.16
• Update ocamlformat to 0.26.0
• Drop support for OCaml compilers < 4.14.0

0.6.0 (2022-11-23)

Added

• Add Fastq module for parsing FASTQ files
• Add ppx_equal and ppx_fields functions to Bio_io.Btab.Parsed.t.

Changed

• Drop Or_error.t returning functions for Records and In_channels (breaking change)

  • The functions with _exn suffix have now become the default (e.g., fold_records_exn is now fold_records).
  • The Or_error.t returning functions are gone. Some were treating truly exceptional events as [Errors] (i.e., if your FASTA file is bad, then you have a major problem!) and others were just not user-friendly.
  • If you don't want to be bothered by exceptions, wrap the function in Or_error.try_with or something similar.

0.5.1 (2022-07-13)

• Fixed issue with project not building under Dune release profile
• Updated OCaml lower bounds in bio_io-dev.opam

0.5.0 (2022-07-13)

Added

• Add Btab_queries module to process Btab files query-by-query rather than hit-by-hit

Changed

Delimited parsing

• Change record names in the Btab module (breaking change)
• Btab.Record.t is now abstract (breaking change)
• No sexp functions on Btab.Record.t (breaking change)
• Drop the Mmseqs module (breaking change)
• Speed up Btab module

Other

• Drop core_kernel from the tests, add base_quickcheck instead
• Drop bisect_ppx, core, and core_bench from opam file. These are now in the bio_io-dev.opam file.
• Drop re2 in favor of re
• Update dune to 3.2
• Update Jane Street libraries to v0.15
• Update ocamlformat to 0.22.4

0.4.0 (2021-12-19)

Fixed

• [Fasta.In_channel] can now read from fifos...e.g., you can pipe the output of gunzip -c directly into a program using the fasta parser and it will be okay.

Added

• Added modules for MMseqs2 and BLAST (e.g., BLAST 6 tab-delimited output)
• Added a couple of example programs in the examples directory

Changed

• Fasta_in_channel is now Fasta.In_channel (breaking change)
• Fasta_record is now Fasta.Record (breaking change)
• Various non-breaking changes

0.3.0 (2021-09-26)

• Add Cigar module for parsing CIGAR strings.

0.2.1 (2021-09-12)

• Specify ppx_expect and ppx_inline_test as test dependencies rather than dev dependencies.

0.2.0 (2021-09-11)

• Require Base rather than Core_kernel
• Add seq_length and to_string_nl functions to Fasta_record module

0.1.2 (2021-08-04)

• Added some benchmarks.
• Sped up fasta parsing.

0.1.1 (2021-05-15)

• Fixed the OCaml min. dependency to 4.08.
• Fixed the lint errors in the opam-ci

0.1.0 (2021-05-14)

Initial release!