Name: biohazard Version: 0.6.9 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) 2010-2017 Udo Stenzel Extra-Source-Files: man/man7/biohazard.7 man/man1/bam-fixpair.1 man/man1/bam-meld.1 man/man1/bam-rewrap.1 man/man1/bam-rmdup.1 man/man1/fastq2bam.1 man/man1/jivebunny.1 man/man1/mt-anno.1 Data-Files: index_db.json Data-Dir: data Cabal-version: >= 1.10 Build-type: Custom Tested-With: GHC == 7.8.4, GHC == 7.10.1, GHC == 8.0.1 source-repository head type: git location: https://bitbucket.org/ustenzel/biohazard.git source-repository this type: git location: https://bitbucket.org/ustenzel/biohazard.git tag: 0.6.9 Flag debug Description: enable additional sanity checks Default: False Manual: True Library Exposed-modules: Bio.Base, Bio.Adna, Bio.Align, Bio.Bam, Bio.Bam.Evan, Bio.Bam.Fastq, Bio.Bam.Filter, Bio.Bam.Header, Bio.Bam.Index, Bio.Bam.Pileup, Bio.Bam.Reader Bio.Bam.Rec, Bio.Bam.Regions, Bio.Bam.Rmdup, Bio.Bam.Trim, Bio.Bam.Writer, Bio.Genocall, Bio.Genocall.Estimators, Bio.Iteratee, Bio.Iteratee.Bgzf, Bio.Iteratee.Builder, Bio.Iteratee.ZLib, Bio.Prelude, Bio.PriorityQueue, Bio.TwoBit, Bio.Util.AD, Bio.Util.AD2, Bio.Util.Jacobi, Bio.Util.Numeric, Bio.Util.Zlib, Paths_biohazard Build-depends: aeson >= 0.7 && < 1.1, aeson-pretty == 0.8.*, async >= 2.0 && < 2.2, attoparsec >= 0.10 && < 0.14, base >= 4.6 && < 4.10, base-prelude == 1.0.*, binary >= 0.7 && < 0.9, 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, hashable >= 1.0 && < 1.3, hybrid-vectors == 0.2.*, 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 >= 0.4.1 && < 0.6, unix >= 2.5 && < 2.8, unordered-containers >= 0.2.3 && < 0.3, vector == 0.11.*, vector-algorithms >= 0.3 && < 1.0, vector-binary-instances == 0.2.*, vector-th-unbox == 0.2.*, zlib >= 0.5 && < 0.7 Ghc-options: -Wall -fprof-auto Default-Language: Haskell2010 Default-Extensions: BangPatterns, DeriveDataTypeable, FlexibleContexts, FlexibleInstances, MultiParamTypeClasses, NoImplicitPrelude, OverloadedStrings, RecordWildCards, TypeSynonymInstances Other-Extensions: CPP, DeriveGeneric, ExistentialQuantification, GeneralizedNewtypeDeriving, PatternGuards, Rank2Types, ScopedTypeVariables, TemplateHaskell, TypeFamilies, TypeOperators 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 -threaded -rtsopts -with-rtsopts=-N -- Type: exitcode-stdio-1.0 -- Main-is: test-biohazard.hs Executable test-pileup Main-is: test-pileup.hs Hs-Source-Dirs: tests Ghc-options: -Wall -fprof-auto Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns Build-depends: async, base, biohazard, bytestring, filepath, unordered-containers, random, text, vector Executable redeye-dar Main-is: redeye-dar.hs Hs-Source-Dirs: tools Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns, RecordWildCards Build-depends: aeson-pretty, async, base, binary, biohazard, bytestring, containers, filepath, unordered-containers, text, vector Executable redeye-single Main-is: redeye-single.hs Ghc-options: -Wall -rtsopts -fprof-auto Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns, RecordWildCards, FlexibleContexts Hs-Source-Dirs: tools Build-depends: aeson, base, binary, biohazard, bytestring, containers, directory, filepath, random, text, unix, unordered-containers, vector Executable redeye-flow Main-is: redeye-flow.hs Ghc-options: -Wall -rtsopts Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns, DeriveGeneric Hs-Source-Dirs: tools Build-depends: aeson, aeson-pretty, base, binary, biohazard, bytestring, containers, directory, shake == 0.15.*, text, unordered-containers, vector Executable afroengineer Main-is: afroengineer.hs Ghc-options: -Wall -rtsopts -- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns, RecordWildCards, Rank2Types Hs-source-dirs: tools Other-Modules: Align, SimpleSeed Build-Depends: base, biohazard, bytestring, containers, directory, unordered-containers, vector Executable bam-fixpair Main-is: bam-fixpair.hs Ghc-options: -Wall -rtsopts -- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns, RecordWildCards, FlexibleContexts Hs-Source-Dirs: tools Build-depends: async, base, binary, biohazard, bytestring, process, stm, transformers, unix, vector Executable bam-meld Main-is: bam-meld.hs Ghc-options: -Wall -rtsopts -- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns, FlexibleContexts Hs-Source-Dirs: tools Build-depends: base, biohazard, bytestring, containers Executable bam-resample Main-is: bam-resample.hs Ghc-options: -Wall -rtsopts -- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns Hs-Source-Dirs: tools Build-depends: base, biohazard, bytestring, random Executable bam-rewrap Main-is: bam-rewrap.hs Ghc-options: -Wall -rtsopts -- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns Hs-Source-Dirs: tools Build-depends: base, biohazard, bytestring, containers Executable bam-rmdup Main-is: bam-rmdup.hs Ghc-options: -Wall -rtsopts -- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns, RecordWildCards, FlexibleContexts Hs-Source-Dirs: tools Build-depends: base, biohazard, bytestring, containers, -- primitive, unordered-containers, vector Executable bam-trim Main-is: bam-trim.hs Ghc-options: -Wall -rtsopts -- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns Hs-Source-Dirs: tools Build-depends: base, biohazard, bytestring Executable fastq2bam Main-is: fastq2bam.hs Ghc-options: -Wall -rtsopts -- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns Hs-Source-Dirs: tools Build-depends: base, biohazard, bytestring, containers, 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 -rtsopts -- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns, TypeFamilies, RecordWildCards Other-modules: Index Build-depends: aeson, base, biohazard, bytestring, containers, directory, random, text, transformers, unordered-containers, vector, vector-algorithms, vector-th-unbox Executable mt-anno Main-is: mt-anno.hs Ghc-options: -Wall -rtsopts -- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns, RecordWildCards Hs-Source-Dirs: tools Other-Modules: Anno, Seqs, Xlate Build-Depends: base, bytestring, biohazard, containers Executable mt-ccheck Main-is: mt-ccheck.hs Ghc-options: -Wall -rtsopts -- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N Default-Language: Haskell2010 Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns, RecordWildCards Hs-Source-Dirs: tools Build-Depends: base, bytestring, biohazard, containers, unordered-containers -- :vim:tw=132: