Name: biohazard Version: 0.6.3 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 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: 0.6.3 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.Glf, Bio.Iteratee, Bio.Iteratee.Bgzf, Bio.Iteratee.Builder, Bio.Iteratee.ZLib, Bio.PriorityQueue, Bio.TwoBit, Bio.Util, Data.Avro Other-modules: Paths_biohazard Build-depends: aeson >= 0.7 && < 0.9, array >= 0.4 && < 0.6, async == 2.0.*, attoparsec >= 0.10 && < 0.13, base >= 4.5 && < 4.9, binary >= 0.7 && < 0.8, bytestring >= 0.10.2 && < 0.11, bytestring-mmap >= 0.2 && < 1.0, containers >= 0.4.1 && < 0.6, 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, 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 && < 0.5, unix == 2.*, 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 afroengineer Main-Is: afroengineer.hs 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 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 Executable bam-meld Main-is: bam-meld.hs 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 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 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 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 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 count-coverage Main-is: count-coverage.hs Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Build-depends: base, biohazard, iteratee Executable dmg-est Main-is: dmg-est.hs Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Other-Modules: AD Build-depends: async, base, biohazard, nonlinear-optimization == 0.3.*, vector Executable fastq2bam Main-is: fastq2bam.hs 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 glf-consensus Main-is: glf-consensus.hs 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, exceptions, iteratee Executable gt-call Main-is: gt-call.hs 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, deepseq, iteratee, text, 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 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 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 executable wiggle-coverage Main-is: wiggle-coverage.hs Hs-Source-Dirs: tools -- Ghc-options: -Wall -auto-all -threaded -rtsopts -with-rtsopts=-N Ghc-options: -Wall -auto-all -rtsopts Build-depends: base, biohazard -- :vim:tw=132: