Name:                bio
Version:             0.4
License:             LGPL
License-file:        LICENSE
Author:              Ketil Malde
Maintainer:          ketil@ii.uib.no

Category:            Bioinformatics
Synopsis:            A bioinformatics library
Description:         This is a collection of data structures and algorithms
                     useful for building bioinformatics-related tools
                     and utilities.
                     .
                     Current list of features includes: a Sequence data type supporting
                     protein and nucleotide sequences and conversion between them.  As of version
		     0.4, different kinds of sequence have different types.  Support for quality
                     data, reading and writing Fasta formatted files, reading TwoBit and
                     phd formats, and Roche/454 SFF files.  Rudimentary (i.e. unoptimized) support
		     for doing alignments - including dynamic adjustment of scores based on sequence quality. 
		     Also Blast output parsing.  Partly implemented single linkage clustering, and
		     multiple alignment.  Reading Gene Ontology (GO) annotations (GOA) and
		     definitions\/hierarchy.
		     .
                     The Darcs repository is at: <http://malde.org/~ketil/biohaskell/biolib>.
Homepage:            http://blog.malde.org/index.php/the-haskell-bioinformatics-library/

Tested-With:         GHC==6.8.2
Build-Type:          Simple
Build-Depends:       base>=3 && <4, QuickCheck<2, binary, tagsoup>=0.4, bytestring >= 0.9.1,
                     containers, array, parallel, parsec, random, old-time, mtl
-- add fps for ghc 6.4.2; change imports in Bio/Sequence/TwoBit.hs if you want QC 2

-- We omit the debian/ and Test/ files because those are for development, not installation.
Data-Files:          README

Exposed-modules:     Bio.Sequence,
                     Bio.Sequence.SeqData,
                     Bio.Sequence.Fasta, Bio.Sequence.FastQ,
		     Bio.Sequence.TwoBit, Bio.Sequence.Phd,
                     Bio.Sequence.Entropy, Bio.Sequence.HashWord,
                     Bio.Sequence.GOA,
                     Bio.Sequence.GeneOntology,
		     Bio.Sequence.KEGG,
		     Bio.Sequence.SFF, Bio.Sequence.SFF_name
                     Bio.Alignment.BlastData, Bio.Alignment.BlastFlat,
                     Bio.Alignment.Blast, Bio.Alignment.BlastXML,
                     Bio.Alignment.AlignData, Bio.Alignment.Matrices,
                     Bio.Alignment.SAlign, Bio.Alignment.AAlign, Bio.Alignment.QAlign
                     Bio.Alignment.Multiple, Bio.Alignment.ACE,
                     Bio.Alignment.Bowtie,
                     Bio.Alignment.Soap,
                     Bio.Clustering,
                     Bio.Util, Bio.Util.Parsex, Bio.Util.TestBase
		 Bio.Location.Strand, Bio.Location.Position,
		 Bio.Location.ContigLocation, Bio.Location.Location, Bio.Location.LocMap,
		 Bio.Location.OnSeq, Bio.Location.SeqLocation, Bio.Location.SeqLocMap,
		 Bio.GFF3.Escape, Bio.GFF3.Feature, Bio.GFF3.FeatureHier, Bio.GFF3.FeatureHierSequences,
		 Bio.GFF3.SGD

extensions:          CPP, ParallelListComp
ghc-options:         -Wall -O2 -fexcess-precision -funbox-strict-fields -auto-all