Name:           dephd
Version:        0.1.6
License:        GPL
License-File:   LICENSE

Author:         Ketil Malde
Maintainer:     Ketil Malde <ketil@malde.org>

Category:       Bioinformatics
Synopsis:       Analyze quality of nucleotide sequences.
Description:    dephd - A simple tool for base calling and quality appraisal.
                .
                Reads files in phd-format (phred output), either specified individually,
                or in a directory (use the --input-dirs option to read directories 
		or --input-list to read from an index file).  Can also read FASTA with an 
		associated quality file.
		.
		Can trim according to Lucy or Phred parameters, can mask by quality, can plot
		graphs (via gnuplot) of sequence quality to a window, or to JPG/EPS files.  Can
		categorize sequences according to overall quality.  Also constructs files suitable for
		submission to dbEST.  More information at <http://blog.malde.org/index.php/2010/09/07/submitting-ests-upstream/>.
		.
		Also provides 'fakequal', a utility to generate bogus quality values,
		which are sometimes needed by less flexible tools.
		.
                The Darcs repository is at <http://malde.org/~ketil/biohaskell/dephd>.

HomePage:	http://malde.org/~ketil/biohaskell/dephd
Build-Type:     Simple
Cabal-Version:	>= 1.6
Tested-with:    GHC==6.12.1
Data-files:     README, TODO

Executable dephd
  Main-Is:        Dephd.hs
  Hs-Source-Dirs: src
  Extensions: 	  BangPatterns
  Build-Depends:  base >= 3 && <5, bio > 0.4, bytestring, regex-compat, process, directory
  Ghc-Options:    -Wall

Executable fakequal
  Main-Is:	  FakeQual.hs
  Hs-Source-Dirs: src
  Build-Depends:  bio > 0.4, cmdargs >= 0.5
  Extensions:	  DeriveDataTypeable