Name:                samtools
Version:             0.1.2
Synopsis:            Binding to the C samtools library
Description:         Binding to the C samtools library, which reads and
                     writes SAM format alignments, both binary and tab-
                     delimited text formats. It also supports rapid access
                     to specific alignments in a sorted BAM file and access
                     to sequences from indexed Fasta files.
License:             MIT
License-file:        LICENSE
Author:              Nicholas Ingolia
Maintainer:          nick@ingolia.org
Category:            Bioinformatics
Homepage:            http://www.ingolia-lab.org/software/samtools/

Build-type:          Simple
Cabal-version:       >=1.4

Extra-source-files: cbits/samtools.c, include/samtools.h,
                    samtools-0.1.13/bgzf.c, samtools-0.1.13/kstring.c, samtools-0.1.13/bam_aux.c, 
                    samtools-0.1.13/bam.c, samtools-0.1.13/bam_import.c, samtools-0.1.13/sam.c,
                    samtools-0.1.13/bam_index.c, samtools-0.1.13/bam_pileup.c, samtools-0.1.13/bam_lpileup.c,
                    samtools-0.1.13/bam_md.c, samtools-0.1.13/glf.c, samtools-0.1.13/razf.c,
                    samtools-0.1.13/faidx.c, samtools-0.1.13/knetfile.c, samtools-0.1.13/bam_sort.c,
                    samtools-0.1.13/sam_header.c, samtools-0.1.13/bam_reheader.c, samtools-0.1.13/kprobaln.c,
                    samtools-0.1.13/bam_maqcns.c, samtools-0.1.13/errmod.c, samtools-0.1.13/kaln.c

Flag Tests
  Description: Build test program
  Default:     False

Library
  Exposed-modules:     Bio.SamTools.Bam, Bio.SamTools.Cigar,
                       Bio.SamTools.BamIndex, Bio.SamTools.FaIdx
  Other-modules:       Bio.SamTools.LowLevel, Bio.SamTools.Internal, C2HS
  Build-depends:       base >= 4.2 && < 5, bytestring, haskell98, vector >= 0.7, seqloc
  Hs-Source-Dirs:      src
  Build-tools:         c2hs
  Include-dirs:        samtools-0.1.13, include
  C-sources:           cbits/samtools.c, 
                       samtools-0.1.13/bgzf.c, samtools-0.1.13/kstring.c, samtools-0.1.13/bam_aux.c, 
                       samtools-0.1.13/bam.c, samtools-0.1.13/bam_import.c, samtools-0.1.13/sam.c,
                       samtools-0.1.13/bam_index.c, samtools-0.1.13/bam_pileup.c, samtools-0.1.13/bam_lpileup.c,
                       samtools-0.1.13/bam_md.c, samtools-0.1.13/glf.c, samtools-0.1.13/razf.c,
                       samtools-0.1.13/faidx.c, samtools-0.1.13/knetfile.c, samtools-0.1.13/bam_sort.c,
                       samtools-0.1.13/sam_header.c, samtools-0.1.13/bam_reheader.c, samtools-0.1.13/kprobaln.c,
                       samtools-0.1.13/bam_maqcns.c, samtools-0.1.13/errmod.c, samtools-0.1.13/kaln.c
  Install-includes:    include/samtools.h,
                       samtools-0.1.13/bam.h, samtools-0.1.13/bam_endian.h, samtools-0.1.13/faidx.h, 
                       samtools-0.1.13/glf.h, samtools-0.1.13/khash.h,
                       samtools-0.1.13/kseq.h, samtools-0.1.13/ksort.h, samtools-0.1.13/kstring.h,
                       samtools-0.1.13/razf.h, samtools-0.1.13/sam.h, samtools-0.1.13/sam_header.h,
                       samtools-0.1.13/bgzf.h, samtools-0.1.13/knetfile.h, samtools-0.1.13/kaln.h,
                       samtools-0.1.13/kprobaln.h, samtools-0.1.13/bam_maqcns.h, samtools-0.1.13/errmod.h
  CC-options:          -g -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
  Extra-libraries:     z
  Ghc-options:         -Wall

Executable samtest
  if !flag(Tests)
     Buildable: False
  Main-is:             SamTest.hs
  Other-modules:       Bio.SamTools.Bam, Bio.SamTools.Cigar,
                       Bio.SamTools.BamIndex, Bio.SamTools.FaIdx,
                       Bio.SamTools.LowLevel, Bio.SamTools.Internal, C2HS
  Build-depends:       base >= 4.2 && < 5, bytestring, haskell98, vector >= 0.7, seqloc, process, filepath
  Hs-Source-Dirs:      src, test
  Build-tools:         c2hs
  Include-dirs:        samtools-0.1.13, include
  C-sources:           cbits/samtools.c, 
                       samtools-0.1.13/bgzf.c, samtools-0.1.13/kstring.c, samtools-0.1.13/bam_aux.c, 
                       samtools-0.1.13/bam.c, samtools-0.1.13/bam_import.c, samtools-0.1.13/sam.c,
                       samtools-0.1.13/bam_index.c, samtools-0.1.13/bam_pileup.c, samtools-0.1.13/bam_lpileup.c,
                       samtools-0.1.13/bam_md.c, samtools-0.1.13/glf.c, samtools-0.1.13/razf.c,
                       samtools-0.1.13/faidx.c, samtools-0.1.13/knetfile.c, samtools-0.1.13/bam_sort.c,
                       samtools-0.1.13/sam_header.c, samtools-0.1.13/bam_reheader.c, samtools-0.1.13/kprobaln.c,
                       samtools-0.1.13/bam_maqcns.c, samtools-0.1.13/errmod.c, samtools-0.1.13/kaln.c
  Install-includes:    include/samtools.h,
                       samtools-0.1.13/bam.h, samtools-0.1.13/bam_endian.h, samtools-0.1.13/faidx.h, 
                       samtools-0.1.13/glf.h, samtools-0.1.13/khash.h,
                       samtools-0.1.13/kseq.h, samtools-0.1.13/ksort.h, samtools-0.1.13/kstring.h,
                       samtools-0.1.13/razf.h, samtools-0.1.13/sam.h, samtools-0.1.13/sam_header.h,
                       samtools-0.1.13/bgzf.h, samtools-0.1.13/knetfile.h, samtools-0.1.13/kaln.h,
                       samtools-0.1.13/kprobaln.h, samtools-0.1.13/bam_maqcns.h, samtools-0.1.13/errmod.h
  CC-options:          -g -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
  Extra-libraries:     z
  Ghc-options:         -Wall