bio-0.3.5: bio.cabal

Name:                bio
Version:             0.3.5
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
                     I've found useful when building various bioinformatics-related tools
                     and utilities.
                     .
                     Current list of features includes: a Sequence data type supporting
                     protein and nucleotide sequences and conversion between them, quality
                     data, reading and writing Fasta formatted files, reading TwoBit and
                     phd formats.  Rudimentary support for doing alignments - including
                     dynamic adjustment of scores based on sequence quality - and 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, 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.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.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