package bio_io
Install
Dune Dependency
Authors
Maintainers
Sources
md5=b1482999e17b5adc24740f95f80b92e3
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CHANGELOG.md.html
Unreleased
NA
0.6.0 (2022-11-23)
Added
Add
Fastq
module for parsing FASTQ filesAdd
ppx_equal
andppx_fields
functions toBio_io.Btab.Parsed.t
.
Changed
Drop
Or_error.t
returning functions forRecords
andIn_channels
(breaking change)The functions with
_exn
suffix have now become the default (e.g.,fold_records_exn
is nowfold_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 onBtab.Record.t
(breaking change)Drop the
Mmseqs
module (breaking change)Speed up Btab module
Other
Drop
core_kernel
from the tests, addbase_quickcheck
insteadDrop
bisect_ppx
,core
, andcore_bench
fromopam
file. These are now in thebio_io-dev.opam
file.Drop
re2
in favor ofre
Update
dune
to3.2
Update Jane Street libraries to
v0.15
Update
ocamlformat
to0.22.4
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 nowFasta.In_channel
(breaking change)Fasta_record
is nowFasta.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
andppx_inline_test
as test dependencies rather than dev dependencies.
0.2.0 (2021-09-11)
Require
Base
rather thanCore_kernel
Add
seq_length
andto_string_nl
functions toFasta_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!