cabal-version: 1.12 -- This file has been generated from package.yaml by hpack version 0.34.4. -- -- see: https://github.com/sol/hpack name: NGLess version: 1.5.0 synopsis: NGLess implements ngless, a DSL for processing sequencing data description: NGLess implements a domain-specific language for processing next generation data, particularly metagenomics. category: Domain Specific Language homepage: https://github.com/ngless-toolkit/ngless#readme bug-reports: https://github.com/ngless-toolkit/ngless/issues author: Luis Pedro Coelho and others (see AUTHORS) maintainer: luis@luispedro.org license: MIT license-file: COPYING build-type: Simple extra-source-files: README.md ChangeLog Html/index.html Html/ngless.css Html/nglessMapStats.html Html/nglessQC.html Html/perBaseQualScores.css NGLess/Interpretation/Count/RefSeqInfoVector.h test_samples/sample.sam.gz test_samples/data_set_repeated.fq test_samples/very_short.gtf Makefile source-repository head type: git location: https://github.com/ngless-toolkit/ngless flag embed description: Embed dependencies manual: False default: False flag static description: Static build manual: False default: False library exposed-modules: BuiltinFunctions BuiltinModules.Argv BuiltinModules.AsReads BuiltinModules.Assemble BuiltinModules.Checks BuiltinModules.LoadDirectory BuiltinModules.ORFFind BuiltinModules.QCStats BuiltinModules.Readlines BuiltinModules.Remove BuiltinModules.Samples Citations CmdArgs Configuration CWL Data.Fasta Data.FastQ Data.FastQ.Utils Data.GFF Data.Sam Dependencies.Embedded Dependencies.Versions ExternalModules FileManagement FileOrStream FileOrStream.Types Interpret Interpretation.Count Interpretation.Count.RefSeqInfoVector Interpretation.CountFile Interpretation.FastQ Interpretation.Map Interpretation.Select Interpretation.Substrim Interpretation.Unique Interpretation.Write JSONScript Language Modules NGLess NGLess.NGError NGLess.NGLEnvironment Output Parse ReferenceDatabases StandardModules.Batch StandardModules.Example StandardModules.Mappers.Bwa StandardModules.Mappers.Minimap2 StandardModules.Mappers.Soap StandardModules.Minimap2 StandardModules.Mocat StandardModules.Motus StandardModules.NGLStdlib StandardModules.Parallel StandardModules.Samtools StandardModules.Soap Tokens Transform Types Utils.Batch Utils.Conduit Utils.Debug Utils.Here Utils.IntGroups Utils.LockFile Utils.Network Utils.Process Utils.ProgressBar Utils.Samtools Utils.Suggestion Utils.Utils Utils.Vector Validation ValidationIO Version other-modules: Paths_NGLess hs-source-dirs: NGLess/ default-extensions: BangPatterns OverloadedStrings LambdaCase TupleSections other-extensions: DeriveDataTypeable TemplateHaskell ghc-options: -Wall -Wcompat -fwarn-tabs -fno-warn-missing-signatures -O2 -fno-full-laziness c-sources: NGLess/Dependencies/embedded.c NGLess/Data/FastQ.c build-depends: MissingH >=1.3 , aeson >=0.9 , ansi-terminal , async , atomic-write >=0.2 , base >=4.12 && <4.16 , bytestring , bytestring-lexing , conduit >=1.3 , conduit-algorithms >=0.0.9.0 , conduit-extra >=1.1.12 , configurator , containers , convertible , data-default , deepseq >=1.3 , directory , edit-distance >=0.2 , either , errors >=2.1 , exceptions , extra >=1.4 , file-embed >=0.0.8 , filemanip >=0.3.6 , filepath >=1.3 , hashable , hashtables , hostname , http-client , http-conduit , inline-c , inline-c-cpp , int-interval-map , mtl >=2.2 , network , optparse-applicative , parsec >=3.1 , primitive >=0.6 , process >=1.2.3 , random-shuffle , regex , resourcet >=1.1 , safe , stm , stm-chans , stm-conduit >=2.7 , strict , tar >=0.5 , tar-conduit >=0.3.2 , template-haskell , text >=1.2 , time >=1.5 , transformers , unix-compat , unliftio , unliftio-core , vector >=0.11 , vector-algorithms , yaml , zlib if os(windows) cpp-options: -DWINDOWS build-depends: atomic-write else build-depends: bzlib-conduit , double-conversion , safeio >=0.0.2 , unix if flag(static) ld-options: -static -pthread default-language: Haskell2010 executable ngless main-is: Main.hs hs-source-dirs: Execs default-extensions: BangPatterns OverloadedStrings LambdaCase TupleSections other-extensions: DeriveDataTypeable TemplateHaskell ghc-options: -Wall -Wcompat -fwarn-tabs -fno-warn-missing-signatures -O2 -fno-full-laziness -threaded -rtsopts "-with-rtsopts=-A64m -n4m -H" c-sources: NGLess/Dependencies/embedded.c NGLess/Data/FastQ.c build-depends: MissingH >=1.3 , NGLess , aeson >=0.9 , ansi-terminal , async , atomic-write >=0.2 , base >=4.12 && <4.16 , bytestring , bytestring-lexing , conduit >=1.3 , conduit-algorithms >=0.0.9.0 , conduit-extra >=1.1.12 , configurator , containers , convertible , data-default , deepseq >=1.3 , directory , edit-distance >=0.2 , either , errors >=2.1 , exceptions , extra >=1.4 , file-embed >=0.0.8 , filemanip >=0.3.6 , filepath >=1.3 , hashable , hashtables , hostname , http-client , http-conduit , inline-c , inline-c-cpp , int-interval-map , mtl >=2.2 , network , optparse-applicative , parsec >=3.1 , primitive >=0.6 , process >=1.2.3 , random-shuffle , regex , resourcet >=1.1 , safe , stm , stm-chans , stm-conduit >=2.7 , strict , tar >=0.5 , tar-conduit >=0.3.2 , template-haskell , text >=1.2 , time >=1.5 , transformers , unix-compat , unliftio , unliftio-core , vector >=0.11 , vector-algorithms , yaml , zlib if os(windows) cpp-options: -DWINDOWS build-depends: atomic-write else build-depends: bzlib-conduit , double-conversion , safeio >=0.0.2 , unix if flag(static) ld-options: -static -pthread if flag(embed) cpp-options: -DBUILD_W_EMBED cc-options: -DBUILD_W_EMBED default-language: Haskell2010 test-suite nglesstest type: exitcode-stdio-1.0 main-is: Tests.hs other-modules: BuiltinFunctions BuiltinModules.Argv BuiltinModules.AsReads BuiltinModules.Assemble BuiltinModules.Checks BuiltinModules.LoadDirectory BuiltinModules.ORFFind BuiltinModules.QCStats BuiltinModules.Readlines BuiltinModules.Remove BuiltinModules.Samples Citations CmdArgs Configuration CWL Data.Fasta Data.FastQ Data.FastQ.Utils Data.GFF Data.Sam Dependencies.Embedded Dependencies.Versions ExternalModules FileManagement FileOrStream FileOrStream.Types Interpret Interpretation.Count Interpretation.Count.RefSeqInfoVector Interpretation.CountFile Interpretation.FastQ Interpretation.Map Interpretation.Select Interpretation.Substrim Interpretation.Unique Interpretation.Write JSONScript Language Modules NGLess NGLess.NGError NGLess.NGLEnvironment Output Parse ReferenceDatabases StandardModules.Batch StandardModules.Example StandardModules.Mappers.Bwa StandardModules.Mappers.Minimap2 StandardModules.Mappers.Soap StandardModules.Minimap2 StandardModules.Mocat StandardModules.Motus StandardModules.NGLStdlib StandardModules.Parallel StandardModules.Samtools StandardModules.Soap Tokens Transform Types Utils.Batch Utils.Conduit Utils.Debug Utils.Here Utils.IntGroups Utils.LockFile Utils.Network Utils.Process Utils.ProgressBar Utils.Samtools Utils.Suggestion Utils.Utils Utils.Vector Validation ValidationIO Version Tests.Count Tests.FastQ Tests.IntGroups Tests.Language Tests.LoadFQDirectory Tests.NGLessAPI Tests.Parse Tests.Samples Tests.Select Tests.Types Tests.Utils Tests.Validation Tests.Vector Tests.Write Paths_NGLess hs-source-dirs: NGLess Tests-Src/ default-extensions: BangPatterns OverloadedStrings LambdaCase TupleSections other-extensions: DeriveDataTypeable TemplateHaskell ghc-options: -Wall -Wcompat -fwarn-tabs -fno-warn-missing-signatures -O2 -fno-full-laziness cpp-options: -DIS_BUILDING_TEST c-sources: NGLess/Dependencies/embedded.c NGLess/Data/FastQ.c build-depends: HUnit >=1.3 , MissingH >=1.3 , QuickCheck >=2.8 , aeson >=0.9 , ansi-terminal , async , atomic-write >=0.2 , base >=4.12 && <4.16 , bytestring , bytestring-lexing , conduit >=1.3 , conduit-algorithms >=0.0.9.0 , conduit-extra >=1.1.12 , configurator , containers , convertible , data-default , deepseq >=1.3 , directory , edit-distance >=0.2 , either , errors >=2.1 , exceptions , extra >=1.4 , file-embed >=0.0.8 , filemanip >=0.3.6 , filepath >=1.3 , hashable , hashtables , hostname , http-client , http-conduit , inline-c , inline-c-cpp , int-interval-map , mtl >=2.2 , network , optparse-applicative , parsec >=3.1 , primitive >=0.6 , process >=1.2.3 , random-shuffle , regex , resourcet >=1.1 , safe , stm , stm-chans , stm-conduit >=2.7 , strict , tar >=0.5 , tar-conduit >=0.3.2 , tasty , tasty-hunit , tasty-quickcheck , tasty-th , template-haskell , text >=1.2 , time >=1.5 , transformers , unix-compat , unliftio , unliftio-core , vector >=0.11 , vector-algorithms , yaml , zlib if os(windows) cpp-options: -DWINDOWS build-depends: atomic-write else build-depends: bzlib-conduit , double-conversion , safeio >=0.0.2 , unix default-language: Haskell2010 benchmark nglessbench type: exitcode-stdio-1.0 main-is: Bench.hs hs-source-dirs: Execs/ default-extensions: BangPatterns OverloadedStrings LambdaCase TupleSections other-extensions: DeriveDataTypeable TemplateHaskell ghc-options: -Wall -Wcompat -fwarn-tabs -fno-warn-missing-signatures -O2 -fno-full-laziness c-sources: NGLess/Dependencies/embedded.c NGLess/Data/FastQ.c build-depends: HUnit >=1.3 , MissingH >=1.3 , NGLess , aeson >=0.9 , ansi-terminal , async , atomic-write >=0.2 , base >=4.12 && <4.16 , bytestring , bytestring-lexing , conduit >=1.3 , conduit-algorithms >=0.0.9.0 , conduit-extra >=1.1.12 , configurator , containers , convertible , criterion , data-default , deepseq >=1.3 , directory , edit-distance >=0.2 , either , errors >=2.1 , exceptions , extra >=1.4 , file-embed >=0.0.8 , filemanip >=0.3.6 , filepath >=1.3 , hashable , hashtables , hostname , http-client , http-conduit , inline-c , inline-c-cpp , int-interval-map , mtl >=2.2 , network , optparse-applicative , parsec >=3.1 , primitive >=0.6 , process >=1.2.3 , random-shuffle , regex , resourcet >=1.1 , safe , stm , stm-chans , stm-conduit >=2.7 , strict , tar >=0.5 , tar-conduit >=0.3.2 , template-haskell , text >=1.2 , time >=1.5 , transformers , unix-compat , unliftio , unliftio-core , vector >=0.11 , vector-algorithms , yaml , zlib if os(windows) cpp-options: -DWINDOWS build-depends: atomic-write else build-depends: bzlib-conduit , double-conversion , safeio >=0.0.2 , unix default-language: Haskell2010