name:                HsHTSLib
version:             1.3.2.0
synopsis:            High level bindings to htslib.
description:         This package provides high level 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 Kai Zhang
category:            Bio
build-type:          Simple
cabal-version:       >=1.10
extra-source-files:
  ChangeLog.md
  htslib-1.3.2/*.h
  htslib-1.3.2/htslib/*.h
  htslib-1.3.2/cram/*.h

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

  build-depends:
      base >=4.8 && <5.0
    , bytestring
    , bytestring-lexing
    , containers
    , conduit-combinators
    , inline-c
    , mtl
    , template-haskell

  hs-source-dirs:      src
  extra-libraries: pthread
  include-dirs:
      htslib-1.3.2

  c-sources:
      src/Bio/HTS.c

      htslib-1.3.2/bgzf.c
      htslib-1.3.2/bgzip.c
      htslib-1.3.2/faidx.c
      htslib-1.3.2/hfile.c
      htslib-1.3.2/hfile_net.c
      htslib-1.3.2/hts.c
      htslib-1.3.2/kfunc.c
      htslib-1.3.2/knetfile.c
      htslib-1.3.2/kstring.c
      htslib-1.3.2/md5.c
      htslib-1.3.2/regidx.c
      htslib-1.3.2/sam.c
      htslib-1.3.2/synced_bcf_reader.c
      htslib-1.3.2/tbx.c
      htslib-1.3.2/vcf.c
      htslib-1.3.2/vcf_sweep.c
      htslib-1.3.2/vcfutils.c

      htslib-1.3.2/cram/cram_codecs.c
      htslib-1.3.2/cram/cram_decode.c
      htslib-1.3.2/cram/cram_encode.c
      htslib-1.3.2/cram/cram_external.c
      htslib-1.3.2/cram/cram_index.c
      htslib-1.3.2/cram/cram_io.c
      htslib-1.3.2/cram/cram_samtools.c
      htslib-1.3.2/cram/cram_stats.c
      htslib-1.3.2/cram/files.c
      htslib-1.3.2/cram/mFILE.c
      htslib-1.3.2/cram/open_trace_file.c
      htslib-1.3.2/cram/pooled_alloc.c
      htslib-1.3.2/cram/rANS_static.c
      htslib-1.3.2/cram/sam_header.c
      htslib-1.3.2/cram/string_alloc.c
      htslib-1.3.2/cram/thread_pool.c
      htslib-1.3.2/cram/vlen.c
      htslib-1.3.2/cram/zfio.c

      -- htslib-1.3.2/tabix.c
      -- htslib-1.3.2/htsfile.c

  default-language:    Haskell2010

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