Name: biohazard Version: 0.6.5 Synopsis: bioinformatics support library Description: This is a collection of modules I separated from various bioinformatics tools. The hope is to make them reusable and easier to maintain. Also includes some of these tools and a bunch that work on mitochondrial sequences. Category: Bioinformatics Homepage: http://github.com/udo-stenzel/biohazard License: BSD3 License-File: LICENSE Author: Udo Stenzel Maintainer: udo.stenzel@eva.mpg.de Copyright: (C) 2010-2015 Udo Stenzel Tested-With: GHC == 7.4.2, GHC == 7.6.3, GHC == 7.8.4, GHC == 7.10.3, GHC == 8.0.1 Extra-Source-Files: man/man7/biohazard.7 man/man1/bam-meld.1 man/man1/bam-rewrap.1 man/man1/bam-rmdup.1 man/man1/jivebunny.1 man/man1/mt-anno.1 doc/genotyping.tex Data-Files: index_db.json Data-Dir: data Cabal-version: >=1.9.2 Build-type: Custom source-repository head type: git location: git://github.com/udo-stenzel/biohazard.git source-repository this type: git location: git://github.com/udo-stenzel/biohazard.git tag: 0.6.5 Library Exposed-modules: Bio.Base, Bio.Align, Bio.Bam, Bio.Bam.Evan, Bio.Bam.Fastq, Bio.Bam.Filter, Bio.Bam.Header, Bio.Bam.Index, Bio.Bam.Pileup, Bio.Bam.Regions, Bio.Bam.Reader Bio.Bam.Rec, Bio.Bam.Rmdup, Bio.Bam.Trim, Bio.Bam.Writer, Bio.Genocall, Bio.Genocall.Adna, Bio.Genocall.AvroFile, Bio.Genocall.Metadata, Bio.Iteratee, Bio.Iteratee.Bgzf, Bio.Iteratee.Builder, Bio.Iteratee.ZLib, Bio.PriorityQueue, Bio.TwoBit, Bio.Util.AD, Bio.Util.AD2, Bio.Util.Numeric, Bio.Util.Regex, Data.MiniFloat, Data.Avro Other-modules: Paths_biohazard Build-depends: aeson >= 0.7 && < 0.9, async == 2.0.*, attoparsec >= 0.10 && < 0.13, base >= 4.5 && < 4.10, binary >= 0.7 && < 0.9, bytestring >= 0.10.2 && < 0.11, bytestring-mmap >= 0.2 && < 1.0, containers >= 0.4.1 && < 0.6, deepseq >= 1.3 && < 1.5, directory >= 1.2 && < 2.0, exceptions >= 0.6 && < 0.9, filepath >= 1.3 && < 2.0, iteratee >= 0.8.9.6 && < 0.8.10, ListLike >= 3.0 && < 5.0, nonlinear-optimization == 0.3.*, primitive >= 0.5 && < 0.7, random >= 1.0 && < 1.2, scientific == 0.3.*, stm == 2.4.*, template-haskell == 2.*, text >= 1.0 && < 2.0, transformers >= 0.3 && < 0.6, unix >= 2.5 && < 2.8, unordered-containers >= 0.2.3 && < 0.3, Vec == 1.*, vector >= 0.9 && < 0.11, vector-algorithms >= 0.3 && < 1.0, vector-th-unbox == 0.2.*, zlib >= 0.5 && < 0.7 Ghc-options: -Wall -auto-all Hs-source-dirs: src Install-Includes: src/cbits/myers_align.h C-sources: src/cbits/myers_align.c CC-options: -fPIC -- Modules not exported by this package. -- Other-modules: -- Extra tools (e.g. alex, hsc2hs, ...) needed to build the source. -- Build-tools: -- Test-Suite test-biohazard -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N -- Type: exitcode-stdio-1.0 -- Main-is: test-biohazard.hs Executable redeye-dar Main-is: redeye-dar.hs Ghc-options: -Wall -auto-all Hs-Source-Dirs: tools Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Build-depends: async, base, biohazard, filepath, unordered-containers, text, vector Executable redeye-div Main-is: redeye-div.hs Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Hs-Source-Dirs: tools Build-depends: async, base, biohazard, filepath, hmatrix == 0.16.*, unordered-containers, text, vector Executable redeye-pileup Main-is: redeye-pileup.hs Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Hs-Source-Dirs: tools Build-depends: aeson, base, biohazard, bytestring, containers, directory, filepath, iteratee, text, unordered-containers, Vec, vector Executable redeye-single Main-is: redeye-single.hs Ghc-options: -Wall -auto-all -rtsopts Hs-Source-Dirs: tools Build-depends: aeson, base, biohazard, bytestring, containers, directory, iteratee, filepath, text, unix, unordered-containers, vector Executable gt-scan Main-is: gt-scan.hs Ghc-options: -Wall -auto-all Hs-Source-Dirs: tools Build-depends: aeson, base, biohazard, bytestring, containers, iteratee, nonlinear-optimization, primitive, strict == 0.3.*, unordered-containers, text, vector -- ------ Executable afroengineer Main-is: afroengineer.hs Ghc-options: -Wall -auto-all Hs-source-dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Other-Modules: Align, SimpleSeed Build-Depends: base, biohazard, bytestring, containers, directory, iteratee, unordered-containers, vector Executable bam-fixpair Main-is: bam-fixpair.hs Ghc-options: -Wall -auto-all Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Build-depends: base, binary, biohazard, bytestring, hashable >= 1.0 && < 1.3, transformers, vector Executable bam-meld Main-is: bam-meld.hs Ghc-options: -Wall -auto-all Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Build-depends: base, biohazard, bytestring, containers Executable bam-resample Main-is: bam-resample.hs Ghc-options: -Wall -auto-all Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Build-depends: base, biohazard, bytestring, random Executable bam-rewrap Main-is: bam-rewrap.hs Ghc-options: -Wall -auto-all Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Build-depends: base, biohazard, bytestring, containers Executable bam-rmdup Main-is: bam-rmdup.hs Ghc-options: -Wall -auto-all Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Build-depends: base, biohazard, bytestring, containers, iteratee, unordered-containers, vector, vector-algorithms Executable bam-trim Main-is: bam-trim.hs Ghc-options: -Wall -auto-all Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Build-depends: base, biohazard, bytestring Executable fastq2bam Main-is: fastq2bam.hs Ghc-options: -Wall -auto-all Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Build-depends: base, biohazard, bytestring, containers, iteratee, vector Executable jivebunny Main-is: jivebunny.hs Hs-Source-Dirs: tools C-sources: src/cbits/jive.c CC-options: -std=c99 -ffast-math -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Other-modules: Index Build-depends: aeson, base, biohazard, bytestring, containers, directory, hashable >= 1.0 && < 1.3, random, text, transformers, unordered-containers, vector, vector-algorithms, vector-th-unbox Executable mt-anno Main-is: mt-anno.hs Ghc-options: -Wall -auto-all Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Other-Modules: Anno, Seqs, Xlate Build-Depends: base, bytestring, biohazard, containers Executable mt-ccheck Main-is: mt-ccheck.hs Ghc-options: -Wall -auto-all Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Build-Depends: base, bytestring, biohazard, containers, unordered-containers -- :vim:tw=132: