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biohazard-tools.cabal
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Name: biohazard-tools
Version: 0.3
Synopsis: bioinformatics tools that work with bam files
Description: A number of command line tools for manipulating bam
files.
Category: Bioinformatics
Homepage: https://bitbucket.org/ustenzel/biohazard-tools
License: BSD3
License-file: LICENSE
Author: Udo Stenzel
Maintainer: u.stenzel@web.de
Copyright: (C) 2010-2017 Udo Stenzel
Extra-source-files: man/man1/bam-fixpair.1
man/man1/bam-mangle.1
man/man1/bam-meld.1
man/man1/bam-rewrap.1
man/man1/bam-rmdup.1
man/man1/expound.1
man/man1/fastq2bam.1
Cabal-version: >= 1.10
Build-type: Custom
Tested-with: GHC == 7.8.4, GHC == 7.10.3, GHC == 8.0.2, GHC == 8.2.1
source-repository head
type: git
location: https://bitbucket.org/ustenzel/biohazard-tools.git
Flag judy
Description: link with Judy library
Default: True
Test-suite bam-sort
Type: exitcode-stdio-1.0
Main-is: bam-sort.hs
Ghc-options: -Wall -rtsopts
Default-Language: Haskell2010
Default-Extensions: NoImplicitPrelude, OverloadedStrings,
BangPatterns, RecordWildCards, FlexibleContexts
Other-Extensions: CPP, Rank2Types
Hs-Source-Dirs: src
Other-modules: Paths_biohazard_tools, PriorityQueue
Include-dirs: cbits
C-sources: cbits/lz4.c
Build-depends: base >= 4.6 && < 4.11,
binary >= 0.8.3 && < 0.9,
biohazard == 1.0.*,
bytestring >= 0.10.2 && < 0.11,
unix >= 2.5 && < 2.8
Executable bam-fixpair
Main-is: bam-fixpair.hs
Ghc-options: -Wall -rtsopts
Default-Language: Haskell2010
Default-Extensions: NoImplicitPrelude, OverloadedStrings,
BangPatterns, RecordWildCards, FlexibleContexts
Other-Extensions: CPP, Rank2Types
Hs-Source-Dirs: src
Other-modules: Paths_biohazard_tools, PriorityQueue
Include-dirs: cbits
C-sources: cbits/lz4.c
Build-depends: async >= 2.0 && < 2.2,
base >= 4.6 && < 4.11,
binary >= 0.8.3 && < 0.9,
biohazard == 1.0.*,
bytestring >= 0.10.2 && < 0.11,
process >= 1.0 && < 1.7,
stm == 2.4.*,
unix >= 2.5 && < 2.8,
vector >= 0.11 && < 0.13
Executable bam-mangle
Main-is: bam-mangle.hs
Ghc-options: -Wall -rtsopts
Default-Language: Haskell2010
Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns
Hs-Source-Dirs: src
Other-modules: Paths_biohazard_tools
Build-depends: base >= 4.6 && < 4.11,
biohazard == 1.0.*,
bytestring >= 0.10.2 && < 0.11,
parsec == 3.*,
random >= 1.0 && < 1.2,
regex-posix >= 0.90 && < 1.0,
transformers >= 0.4.1 && < 0.6,
unordered-containers >= 0.2.3 && < 0.3,
vector >= 0.11 && < 0.13
Executable bam-meld
Main-is: bam-meld.hs
Ghc-options: -Wall -rtsopts
Default-Language: Haskell2010
Default-Extensions: NoImplicitPrelude, OverloadedStrings,
BangPatterns, FlexibleContexts
Hs-Source-Dirs: src
Other-modules: Paths_biohazard_tools
Build-depends: base >= 4.6 && < 4.11,
biohazard == 1.0.*,
bytestring >= 0.10.2 && < 0.11,
containers >= 0.4.1 && < 0.6
Executable bam-resample
Main-is: bam-resample.hs
Ghc-options: -Wall -rtsopts
Default-Language: Haskell2010
Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns
Hs-Source-Dirs: src
Other-modules: Paths_biohazard_tools
Build-depends: base >= 4.6 && < 4.11,
biohazard == 1.0.*,
bytestring >= 0.10.2 && < 0.11,
random >= 1.0 && < 1.2
Executable bam-rewrap
Main-is: bam-rewrap.hs
Ghc-options: -Wall -rtsopts
Default-Language: Haskell2010
Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns
Hs-Source-Dirs: src
Other-modules: Paths_biohazard_tools
Build-depends: base >= 4.6 && < 4.11,
biohazard == 1.0.*,
bytestring >= 0.10.2 && < 0.11,
containers >= 0.4.1 && < 0.6
Executable bam-rmdup
Main-is: bam-rmdup.hs
Ghc-options: -Wall -rtsopts
Default-Language: Haskell2010
Default-Extensions: NoImplicitPrelude, OverloadedStrings,
BangPatterns, RecordWildCards, FlexibleContexts
Hs-Source-Dirs: src
Other-modules: Paths_biohazard_tools, PriorityQueue
Include-dirs: cbits
C-sources: cbits/lz4.c
Build-depends: base >= 4.6 && < 4.11,
binary >= 0.8.3 && < 0.9,
biohazard == 1.0.*,
bytestring >= 0.10.2 && < 0.11,
containers >= 0.4.1 && < 0.6,
unordered-containers >= 0.2.3 && < 0.3,
vector >= 0.11 && < 0.13
Executable bam-trim
Main-is: bam-trim.hs
Ghc-options: -Wall -rtsopts
Default-Language: Haskell2010
Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns
Hs-Source-Dirs: src
Other-modules: Paths_biohazard_tools
Build-depends: base >= 4.6 && < 4.11,
biohazard == 1.0.*,
bytestring >= 0.10.2 && < 0.11
Executable expound
Main-is: expound.hs
Ghc-options: -Wall -rtsopts
Default-Language: Haskell2010
Default-Extensions: NoImplicitPrelude, OverloadedStrings,
BangPatterns, Rank2Types, LambdaCase
Hs-Source-Dirs: src
Other-modules: Diet, FormattedIO, Network, Symtab, Paths_biohazard_tools
Build-depends: async >= 2.0 && < 2.2,
base >= 4.6 && < 4.11,
binary >= 0.8.3 && < 0.9,
biohazard == 1.0.*,
bytestring >= 0.10.2 && < 0.11,
exceptions >= 0.6 && < 0.9,
filepath >= 1.3 && < 1.5,
network >= 2.3 && < 3.0,
transformers >= 0.4.1 && < 0.6,
unordered-containers >= 0.2.3 && < 0.3,
vector >= 0.11 && < 0.13
if flag(judy)
Extra-libraries: Judy
C-sources: src/withJudy/diet.c
Hs-Source-Dirs: src/withJudy
Other-Extensions: ForeignFunctionInterface, EmptyDataDecls
else
Build-depends: containers >= 0.4.1 && < 0.6
Hs-Source-Dirs: src/withoutJudy
Executable fastq2bam
Main-is: fastq2bam.hs
Ghc-options: -Wall -rtsopts
Default-Language: Haskell2010
Default-Extensions: NoImplicitPrelude, OverloadedStrings, BangPatterns
Hs-Source-Dirs: src
Other-modules: Paths_biohazard_tools
Build-depends: base >= 4.6 && < 4.11,
biohazard == 1.0.*,
bytestring >= 0.10.2 && < 0.11,
containers >= 0.4.1 && < 0.6,
vector >= 0.11 && < 0.13
-- :vim:tw=132: