HsHTSLib-1.9.2: HsHTSLib.cabal

name:                HsHTSLib
version:             1.9.2
synopsis:            Bindings to htslib.
description:         This package provides bindings to htslib, a library
                     for processing high throughput DNA sequencing data.
license:             MIT
license-file:        LICENSE
author:              Kai Zhang
maintainer:          kai@kzhang.org
copyright:           (c) 2016-2019 Kai Zhang
category:            Bio
build-type:          Simple
cabal-version:       >=1.10
extra-source-files:
  README.md
  ChangeLog.md

  -- C header files
  htslib-1.9/*.h
  htslib-1.9/htslib/*.h
  htslib-1.9/cram/*.h
  htslib-1.9/os/*.h

  -- TEST DATA
  tests/data/example.bam
  tests/data/example.sam
  tests/data/single_end.bam
  tests/data/single_end_dedup.bam

library
  ghc-options:         -Wall
  exposed-modules:
    Bio.HTS
    Bio.HTS.Internal
    Bio.HTS.Types
    Bio.HTS.BAM
    Bio.HTS.Utils

  build-depends:
      base >= 4.10 && < 5.0
    , bytestring
    , bytestring-lexing
    , conduit >= 1.3.0
    , containers

  hs-source-dirs:      src
  build-tools:         c2hs >= 0.25.0
  extra-libraries: pthread z
  include-dirs: htslib-1.9
  c-sources:
      cbits/hs_htslib.c

      htslib-1.9/bcf_sr_sort.c
      htslib-1.9/bgzf.c
      htslib-1.9/bgzip.c
      htslib-1.9/errmod.c
      htslib-1.9/faidx.c
      htslib-1.9/hfile.c
      --htslib-1.9/hfile_gcs.c
      --htslib-1.9/hfile_libcurl.c
      htslib-1.9/hfile_net.c
      --htslib-1.9/hfile_s3.c
      htslib-1.9/hts.c
      -- htslib-1.9/htsfile.c
      htslib-1.9/hts_os.c
      htslib-1.9/kfunc.c
      htslib-1.9/knetfile.c
      htslib-1.9/kstring.c
      htslib-1.9/md5.c
      htslib-1.9/multipart.c
      -- htslib-1.9/plugin.c
      htslib-1.9/probaln.c
      htslib-1.9/realn.c
      htslib-1.9/regidx.c
      htslib-1.9/sam.c
      htslib-1.9/synced_bcf_reader.c
      -- htslib-1.9/tabix.c
      htslib-1.9/tbx.c
      htslib-1.9/textutils.c
      htslib-1.9/thread_pool.c
      htslib-1.9/vcf.c
      htslib-1.9/vcf_sweep.c
      htslib-1.9/vcfutils.c

      htslib-1.9/cram/cram_codecs.c
      htslib-1.9/cram/cram_decode.c
      htslib-1.9/cram/cram_encode.c
      htslib-1.9/cram/cram_external.c
      htslib-1.9/cram/cram_index.c
      htslib-1.9/cram/cram_io.c
      htslib-1.9/cram/cram_samtools.c
      htslib-1.9/cram/cram_stats.c
      htslib-1.9/cram/files.c
      htslib-1.9/cram/mFILE.c
      htslib-1.9/cram/open_trace_file.c
      htslib-1.9/cram/pooled_alloc.c
      htslib-1.9/cram/rANS_static.c
      htslib-1.9/cram/sam_header.c
      htslib-1.9/cram/string_alloc.c

      -- htslib-1.9/os/rand.c

  default-language:    Haskell2010

test-suite tests
  type: exitcode-stdio-1.0
  hs-source-dirs: tests
  main-is: Main.hs
  other-modules:

  default-language:    Haskell2010
  build-depends:
      base
    , HsHTSLib
    , bytestring
    , vector
    , tasty
    , tasty-golden
    , tasty-hunit
    , conduit

source-repository  head
  type: git
  location: https://github.com/kaizhang/HsHTSLib.git