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hs-samtools.cabal
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cabal-version: 3.0
-- The cabal-version field refers to the version of the .cabal specification,
-- and can be different from the cabal-install (the tool) version and the
-- Cabal (the library) version you are using. As such, the Cabal (the library)
-- version used must be equal or greater than the version stated in this field.
-- Starting from the specification version 2.2, the cabal-version field must be
-- the first thing in the cabal file.
-- Initial package description 'hs-samtools' generated by
-- 'cabal init'. For further documentation, see:
-- http://haskell.org/cabal/users-guide/
--
-- The name of the package.
name: hs-samtools
-- The package version.
-- See the Haskell package versioning policy (PVP) for standards
-- guiding when and how versions should be incremented.
-- https://pvp.haskell.org
-- PVP summary: +-+-------- breaking API changes
-- | | +----- non-breaking API additions
-- | | | +--- code changes with no API change
version: 0.10.0.3
-- A short (one-line) description of the package.
synopsis: Read and write SAM, BAM, and CRAM files.
-- A longer description of the package.
description: A SAM, BAM, and CRAM file decoder/encoded along with various related functionality associated with these file formats.
-- URL for the project homepage or repository.
homepage: https://github.com/Matthew-Mosior/hs-samtools
-- The license under which the package is released.
license: BSD-3-Clause
-- The file containing the license text.
license-file: LICENSE
-- The package author(s).
author: Matthew Mosior
-- An email address to which users can send suggestions, bug reports, and patches.
maintainer: [email protected]
-- Where to submit bugs.
bug-reports: https://github.com/Matthew-Mosior/hs-samtools/issues
-- A copyright notice.
-- copyright:
category: Bioinformatics
build-type: Simple
-- Extra doc files to be distributed with the package, such as a CHANGELOG or a README.
extra-doc-files: CHANGELOG.md
-- Extra source files to be distributed with the package, such as examples, or a tutorial module.
-- extra-source-files:
common warnings
ghc-options: -Wall
library
-- Import common warning flags.
import: warnings
-- Modules exported by the library.
exposed-modules: Data.BAM.Version1_6.Base,
Data.BAM.Version1_6.BAM,
Data.BAM.Version1_6.BAM.BAMAlignments,
Data.BAM.Version1_6.BAM.BAMHeader,
Data.BAM.Version1_6.BAM.Alignment,
Data.BAM.Version1_6.BAM.Alignment.Base,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.AOPT,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigCOPT,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigIOPT,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigSOPT,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallCOPT,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallIOPT,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallSOPT,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.FOPT,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.HOPT,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.ZOPT,
Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BOPT,
Data.BAM.Version1_6.BAM.Header,
Data.BAM.Version1_6.BAM.Header.CO,
Data.BAM.Version1_6.BAM.Header.HD,
Data.BAM.Version1_6.BAM.Header.PG,
Data.BAM.Version1_6.BAM.Header.RG,
Data.BAM.Version1_6.BAM.Header.SQ,
Data.BAM.Version1_6.BAM.ReferenceInformation,
Data.BAM.Version1_6.BAM.ReferenceInformation.Base,
Data.BAM.Version1_6.BGZFBlock,
Data.BAM.Version1_6.GZipHeader,
Data.BAM.Version1_6.Read.Base,
Data.BAM.Version1_6.Read.Error,
Data.BAM.Version1_6.Read.Parser.BGZFBlock,
Data.BAM.Version1_6.Read.Parser.BAM.Base,
Data.BAM.Version1_6.Read.Parser.BAM.BAMAlignments,
Data.BAM.Version1_6.Read.Parser.BAM.BAMHeader,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.Base,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.AOPT,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigCOPT,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigIOPT,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigSOPT,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallCOPT,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallIOPT,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallSOPT,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.FOPT,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.HOPT,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.ZOPT,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BOPT,
Data.BAM.Version1_6.Read.Parser.BAM.ReferenceInformation.Base,
Data.BAM.Version1_6.Write.Base,
Data.BAM.Version1_6.Write.Error,
Data.SAM.Version1_6.Base,
Data.SAM.Version1_6.Alignment,
Data.SAM.Version1_6.Alignment.Base,
Data.SAM.Version1_6.Alignment.OptionalFields.Base,
Data.SAM.Version1_6.Alignment.OptionalFields.AOPT,
Data.SAM.Version1_6.Alignment.OptionalFields.FOPT,
Data.SAM.Version1_6.Alignment.OptionalFields.HOPT,
Data.SAM.Version1_6.Alignment.OptionalFields.IOPT,
Data.SAM.Version1_6.Alignment.OptionalFields.ZOPT,
Data.SAM.Version1_6.Alignment.OptionalFields.BOPT,
Data.SAM.Version1_6.Header,
Data.SAM.Version1_6.Header.CO,
Data.SAM.Version1_6.Header.HD,
Data.SAM.Version1_6.Header.PG,
Data.SAM.Version1_6.Header.RG,
Data.SAM.Version1_6.Header.SQ,
Data.SAM.Version1_6.Read.Base,
Data.SAM.Version1_6.Read.Error,
Data.SAM.Version1_6.Read.Parser.Alignment.Base,
Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.AOPT,
Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.IOPT,
Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.FOPT,
Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.ZOPT,
Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.HOPT,
Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.BOPT,
Data.SAM.Version1_6.Read.Parser.Header.HD.Base,
Data.SAM.Version1_6.Read.Parser.Header.HD.VN,
Data.SAM.Version1_6.Read.Parser.Header.HD.SO,
Data.SAM.Version1_6.Read.Parser.Header.HD.GO,
Data.SAM.Version1_6.Read.Parser.Header.HD.SS,
Data.SAM.Version1_6.Read.Parser.Header.SQ.Base,
Data.SAM.Version1_6.Read.Parser.Header.SQ.SN,
Data.SAM.Version1_6.Read.Parser.Header.SQ.LN,
Data.SAM.Version1_6.Read.Parser.Header.SQ.AH,
Data.SAM.Version1_6.Read.Parser.Header.SQ.AN,
Data.SAM.Version1_6.Read.Parser.Header.SQ.AS,
Data.SAM.Version1_6.Read.Parser.Header.SQ.DS,
Data.SAM.Version1_6.Read.Parser.Header.SQ.M5,
Data.SAM.Version1_6.Read.Parser.Header.SQ.SP,
Data.SAM.Version1_6.Read.Parser.Header.SQ.TP,
Data.SAM.Version1_6.Read.Parser.Header.SQ.UR,
Data.SAM.Version1_6.Read.Parser.Header.RG.Base,
Data.SAM.Version1_6.Read.Parser.Header.RG.ID,
Data.SAM.Version1_6.Read.Parser.Header.RG.BC,
Data.SAM.Version1_6.Read.Parser.Header.RG.CN,
Data.SAM.Version1_6.Read.Parser.Header.RG.DS,
Data.SAM.Version1_6.Read.Parser.Header.RG.DT,
Data.SAM.Version1_6.Read.Parser.Header.RG.FO,
Data.SAM.Version1_6.Read.Parser.Header.RG.KS,
Data.SAM.Version1_6.Read.Parser.Header.RG.LB,
Data.SAM.Version1_6.Read.Parser.Header.RG.PG,
Data.SAM.Version1_6.Read.Parser.Header.RG.PI,
Data.SAM.Version1_6.Read.Parser.Header.RG.PL,
Data.SAM.Version1_6.Read.Parser.Header.RG.PM,
Data.SAM.Version1_6.Read.Parser.Header.RG.PU,
Data.SAM.Version1_6.Read.Parser.Header.RG.SM,
Data.SAM.Version1_6.Read.Parser.Header.PG.Base,
Data.SAM.Version1_6.Read.Parser.Header.PG.ID,
Data.SAM.Version1_6.Read.Parser.Header.PG.PN,
Data.SAM.Version1_6.Read.Parser.Header.PG.CL,
Data.SAM.Version1_6.Read.Parser.Header.PG.PP,
Data.SAM.Version1_6.Read.Parser.Header.PG.DS,
Data.SAM.Version1_6.Read.Parser.Header.PG.VN,
Data.SAM.Version1_6.Read.Parser.Header.CO.Base,
Data.SAM.Version1_6.Write.Base
-- Modules included in this library but not exported.
other-modules: Data.BAM.Version1_6.Internal,
Data.BAM.Version1_6.Read.Parser.BAM.Alignment.Internal,
Data.BAM.Version1_6.Write.Internal,
Data.SAM.Version1_6.Internal
-- LANGUAGE extensions used by modules in this package.
-- other-extensions:
-- Other library packages from which modules are imported.
build-depends: base >= 4.18.2 && < 4.19,
array >= 0.5.6 && < 0.6,
ascii >= 1.7.0 && < 1.8,
base16 >= 1.0 && < 1.1,
binary >= 0.8.9 && < 0.9,
bytestring >= 0.11.5 && < 0.12,
containers >= 0.6.7 && < 0.7,
attoparsec >= 0.14.4 && < 0.15,
bitvec >= 1.1.5 && < 1.2,
crypton >= 1.0.0 && < 1.1,
deepseq >= 1.4.8 && < 1.5,
digest >= 0.0.2 && < 0.1,
generic-deriving >= 1.14.5 && < 1.15,
mason >= 0.2.6 && < 0.3,
parsers >= 0.12.11 && < 0.13,
parser-combinators >= 1.3.0 && < 1.4,
pcre-heavy >= 1.0.0 && < 1.1,
regex-tdfa >= 1.3.2 && < 1.4,
streamly >= 0.10.0 && < 0.11,
streamly-bytestring >= 0.2.1 && < 0.3,
streamly-core >= 0.2.1 && < 0.3,
zlib >= 0.7.1 && < 0.8
-- Directories containing source files.
hs-source-dirs: src
-- Base language which the package is written in.
default-language: Haskell2010
test-suite hs-samtools-test
-- Import common warning flags.
import: warnings
-- Base language which the package is written in.
default-language: Haskell2010
-- Modules included in this executable, other than Main.
-- other-modules:
-- LANGUAGE extensions used by modules in this package.
-- other-extensions:
-- The interface type and version of the test suite.
type: exitcode-stdio-1.0
-- Directories containing source files.
hs-source-dirs: test
-- The entrypoint to the test suite.
main-is: Main.hs
-- Test dependencies.
build-depends: base,
bytestring,
containers,
hspec,
hs-samtools