Safe Haskell	Safe-Inferred
Language	Haskell2010

Poseidon.SequencingSource

Synopsis

newtype SeqSourceRows = SeqSourceRows {
- getSeqSourceRowList :: [SeqSourceRow]
}
data SeqSourceRow = SeqSourceRow {
- sPoseidonID :: Maybe (ListColumn String)
- sUDG :: Maybe SSFUDG
- sLibraryBuilt :: Maybe SSFLibraryBuilt
- sSampleAccession :: Maybe SSFAccessionIDSample
- sStudyAccession :: Maybe SSFAccessionIDStudy
- sRunAccession :: Maybe SSFAccessionIDRun
- sSampleAlias :: Maybe SSFSampleAlias
- sSecondarySampleAccession :: Maybe SSFSecondarySampleAccession
- sFirstPublic :: Maybe SSFFirstPublicSimpleDate
- sLastUpdated :: Maybe SSFLastUpdatedSimpleDate
- sInstrumentModel :: Maybe SSFInstrumentModel
- sLibraryLayout :: Maybe SSFLibraryLayout
- sLibrarySource :: Maybe SSFLibrarySource
- sInstrumentPlatform :: Maybe SSFInstrumentPlatform
- sLibraryName :: Maybe SSFLibraryName
- sLibraryStrategy :: Maybe SSFLibraryStrategy
- sFastqFTP :: Maybe (ListColumn SSFFastqFTPURI)
- sFastqASPERA :: Maybe (ListColumn SSFFastqASPERAURI)
- sFastqBytes :: Maybe (ListColumn SSFFastqBytes)
- sFastqMD5 :: Maybe (ListColumn SSFFastqMD5)
- sReadCount :: Maybe SSFReadCount
- sSubmittedFTP :: Maybe (ListColumn SSFSubmittedFTPURI)
- sAdditionalColumns :: CsvNamedRecord
}
seqSourceHeader :: [ByteString]
seqSourceHeaderString :: [String]
seqSourceRefHashMap :: HashMap ByteString ()
writeSeqSourceFile :: FilePath -> SeqSourceRows -> IO ()
readSeqSourceFile :: FilePath -> PoseidonIO SeqSourceRows
readSeqSourceFileRow :: FilePath -> (Int, ByteString) -> PoseidonIO (Either PoseidonException SeqSourceRow)
warnSeqSourceConsistency :: FilePath -> SeqSourceRows -> PoseidonIO ()
checkRunsUnique :: SeqSourceRows -> Bool
checkAtLeastOnePoseidonID :: SeqSourceRows -> Bool

Documentation

newtype SeqSourceRows Source #

A data type to represent a seqSourceFile

Constructors

SeqSourceRows
Fields getSeqSourceRowList :: [SeqSourceRow]

Instances

Instances details

Monoid SeqSourceRows Source #
Instance details Defined in Poseidon.SequencingSource Methods mempty :: SeqSourceRows # mappend :: SeqSourceRows -> SeqSourceRows -> SeqSourceRows # mconcat :: [SeqSourceRows] -> SeqSourceRows #
Semigroup SeqSourceRows Source #
Instance details Defined in Poseidon.SequencingSource Methods (<>) :: SeqSourceRows -> SeqSourceRows -> SeqSourceRows # sconcat :: NonEmpty SeqSourceRows -> SeqSourceRows # stimes :: Integral b => b -> SeqSourceRows -> SeqSourceRows #
Generic SeqSourceRows Source #
Instance details Defined in Poseidon.SequencingSource Associated Types type Rep SeqSourceRows :: Type -> Type # Methods from :: SeqSourceRows -> Rep SeqSourceRows x # to :: Rep SeqSourceRows x -> SeqSourceRows #
Show SeqSourceRows Source #
Instance details Defined in Poseidon.SequencingSource Methods showsPrec :: Int -> SeqSourceRows -> ShowS # show :: SeqSourceRows -> String # showList :: [SeqSourceRows] -> ShowS #
Eq SeqSourceRows Source #
Instance details Defined in Poseidon.SequencingSource Methods (==) :: SeqSourceRows -> SeqSourceRows -> Bool # (/=) :: SeqSourceRows -> SeqSourceRows -> Bool #
type Rep SeqSourceRows Source #
Instance details Defined in Poseidon.SequencingSource type Rep SeqSourceRows = D1 ('MetaData "SeqSourceRows" "Poseidon.SequencingSource" "poseidon-hs-1.6.7.3-GB1MYUceETwBAiXCnu0Oii" 'True) (C1 ('MetaCons "SeqSourceRows" 'PrefixI 'True) (S1 ('MetaSel ('Just "getSeqSourceRowList") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [SeqSourceRow])))

data SeqSourceRow Source #

A data type to represent a row in the seqSourceFile See https://github.com/poseidon-framework/poseidon2-schema/blob/master/seqSourceFile_columns.tsv for more details

Constructors

SeqSourceRow

Fields

sPoseidonID :: Maybe (ListColumn String)
sUDG :: Maybe SSFUDG
sLibraryBuilt :: Maybe SSFLibraryBuilt
sSampleAccession :: Maybe SSFAccessionIDSample
sStudyAccession :: Maybe SSFAccessionIDStudy
sRunAccession :: Maybe SSFAccessionIDRun
sSampleAlias :: Maybe SSFSampleAlias
sSecondarySampleAccession :: Maybe SSFSecondarySampleAccession
sFirstPublic :: Maybe SSFFirstPublicSimpleDate
sLastUpdated :: Maybe SSFLastUpdatedSimpleDate
sInstrumentModel :: Maybe SSFInstrumentModel
sLibraryLayout :: Maybe SSFLibraryLayout
sLibrarySource :: Maybe SSFLibrarySource
sInstrumentPlatform :: Maybe SSFInstrumentPlatform
sLibraryName :: Maybe SSFLibraryName
sLibraryStrategy :: Maybe SSFLibraryStrategy
sFastqFTP :: Maybe (ListColumn SSFFastqFTPURI)
sFastqASPERA :: Maybe (ListColumn SSFFastqASPERAURI)
sFastqBytes :: Maybe (ListColumn SSFFastqBytes)
sFastqMD5 :: Maybe (ListColumn SSFFastqMD5)
sReadCount :: Maybe SSFReadCount
sSubmittedFTP :: Maybe (ListColumn SSFSubmittedFTPURI)
sAdditionalColumns :: CsvNamedRecord

Instances

Instances details

Generic SeqSourceRow Source #
Instance details Defined in Poseidon.SequencingSource Associated Types type Rep SeqSourceRow :: Type -> Type # Methods from :: SeqSourceRow -> Rep SeqSourceRow x # to :: Rep SeqSourceRow x -> SeqSourceRow #
Show SeqSourceRow Source #
Instance details Defined in Poseidon.SequencingSource Methods showsPrec :: Int -> SeqSourceRow -> ShowS # show :: SeqSourceRow -> String # showList :: [SeqSourceRow] -> ShowS #
DefaultOrdered SeqSourceRow Source #
Instance details Defined in Poseidon.SequencingSource Methods headerOrder :: SeqSourceRow -> Header
FromNamedRecord SeqSourceRow Source #
Instance details Defined in Poseidon.SequencingSource Methods parseNamedRecord :: NamedRecord -> Parser SeqSourceRow
ToNamedRecord SeqSourceRow Source #
Instance details Defined in Poseidon.SequencingSource Methods toNamedRecord :: SeqSourceRow -> NamedRecord
Generic SeqSourceRow Source #
Instance details Defined in Poseidon.SequencingSource Associated Types type Code SeqSourceRow :: [[Type]] Methods from :: SeqSourceRow -> Rep SeqSourceRow to :: Rep SeqSourceRow -> SeqSourceRow
HasDatatypeInfo SeqSourceRow Source #
Instance details Defined in Poseidon.SequencingSource Associated Types type DatatypeInfoOf SeqSourceRow :: DatatypeInfo Methods datatypeInfo :: proxy SeqSourceRow -> DatatypeInfo (Code SeqSourceRow)
Eq SeqSourceRow Source #
Instance details Defined in Poseidon.SequencingSource Methods (==) :: SeqSourceRow -> SeqSourceRow -> Bool # (/=) :: SeqSourceRow -> SeqSourceRow -> Bool #
type Rep SeqSourceRow Source #
Instance details Defined in Poseidon.SequencingSource type Rep SeqSourceRow = D1 ('MetaData "SeqSourceRow" "Poseidon.SequencingSource" "poseidon-hs-1.6.7.3-GB1MYUceETwBAiXCnu0Oii" 'False) (C1 ('MetaCons "SeqSourceRow" 'PrefixI 'True) ((((S1 ('MetaSel ('Just "sPoseidonID") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn String))) :: S1 ('MetaSel ('Just "sUDG") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFUDG))) :: (S1 ('MetaSel ('Just "sLibraryBuilt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFLibraryBuilt)) :: (S1 ('MetaSel ('Just "sSampleAccession") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFAccessionIDSample)) :: S1 ('MetaSel ('Just "sStudyAccession") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFAccessionIDStudy))))) :: ((S1 ('MetaSel ('Just "sRunAccession") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFAccessionIDRun)) :: (S1 ('MetaSel ('Just "sSampleAlias") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFSampleAlias)) :: S1 ('MetaSel ('Just "sSecondarySampleAccession") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFSecondarySampleAccession)))) :: (S1 ('MetaSel ('Just "sFirstPublic") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFFirstPublicSimpleDate)) :: (S1 ('MetaSel ('Just "sLastUpdated") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFLastUpdatedSimpleDate)) :: S1 ('MetaSel ('Just "sInstrumentModel") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFInstrumentModel)))))) :: (((S1 ('MetaSel ('Just "sLibraryLayout") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFLibraryLayout)) :: (S1 ('MetaSel ('Just "sLibrarySource") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFLibrarySource)) :: S1 ('MetaSel ('Just "sInstrumentPlatform") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFInstrumentPlatform)))) :: (S1 ('MetaSel ('Just "sLibraryName") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFLibraryName)) :: (S1 ('MetaSel ('Just "sLibraryStrategy") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFLibraryStrategy)) :: S1 ('MetaSel ('Just "sFastqFTP") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn SSFFastqFTPURI)))))) :: ((S1 ('MetaSel ('Just "sFastqASPERA") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn SSFFastqASPERAURI))) :: (S1 ('MetaSel ('Just "sFastqBytes") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn SSFFastqBytes))) :: S1 ('MetaSel ('Just "sFastqMD5") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn SSFFastqMD5))))) :: (S1 ('MetaSel ('Just "sReadCount") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SSFReadCount)) :: (S1 ('MetaSel ('Just "sSubmittedFTP") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn SSFSubmittedFTPURI))) :: S1 ('MetaSel ('Just "sAdditionalColumns") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 CsvNamedRecord)))))))
type Code SeqSourceRow Source #
Instance details Defined in Poseidon.SequencingSource type Code SeqSourceRow = '['[Maybe (ListColumn String), Maybe SSFUDG, Maybe SSFLibraryBuilt, Maybe SSFAccessionIDSample, Maybe SSFAccessionIDStudy, Maybe SSFAccessionIDRun, Maybe SSFSampleAlias, Maybe SSFSecondarySampleAccession, Maybe SSFFirstPublicSimpleDate, Maybe SSFLastUpdatedSimpleDate, Maybe SSFInstrumentModel, Maybe SSFLibraryLayout, Maybe SSFLibrarySource, Maybe SSFInstrumentPlatform, Maybe SSFLibraryName, Maybe SSFLibraryStrategy, Maybe (ListColumn SSFFastqFTPURI), Maybe (ListColumn SSFFastqASPERAURI), Maybe (ListColumn SSFFastqBytes), Maybe (ListColumn SSFFastqMD5), Maybe SSFReadCount, Maybe (ListColumn SSFSubmittedFTPURI), CsvNamedRecord]]
type DatatypeInfoOf SeqSourceRow Source #
Instance details Defined in Poseidon.SequencingSource type DatatypeInfoOf SeqSourceRow = 'ADT "Poseidon.SequencingSource" "SeqSourceRow" '['Record "SeqSourceRow" '['FieldInfo "sPoseidonID", 'FieldInfo "sUDG", 'FieldInfo "sLibraryBuilt", 'FieldInfo "sSampleAccession", 'FieldInfo "sStudyAccession", 'FieldInfo "sRunAccession", 'FieldInfo "sSampleAlias", 'FieldInfo "sSecondarySampleAccession", 'FieldInfo "sFirstPublic", 'FieldInfo "sLastUpdated", 'FieldInfo "sInstrumentModel", 'FieldInfo "sLibraryLayout", 'FieldInfo "sLibrarySource", 'FieldInfo "sInstrumentPlatform", 'FieldInfo "sLibraryName", 'FieldInfo "sLibraryStrategy", 'FieldInfo "sFastqFTP", 'FieldInfo "sFastqASPERA", 'FieldInfo "sFastqBytes", 'FieldInfo "sFastqMD5", 'FieldInfo "sReadCount", 'FieldInfo "sSubmittedFTP", 'FieldInfo "sAdditionalColumns"]] '['['StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy]]

seqSourceHeader :: [ByteString] Source #

seqSourceHeaderString :: [String] Source #

seqSourceRefHashMap :: HashMap ByteString () Source #

writeSeqSourceFile :: FilePath -> SeqSourceRows -> IO () Source #

A function to write one seqSourceFile

readSeqSourceFile :: FilePath -> PoseidonIO SeqSourceRows Source #

A function to read one seqSourceFile

readSeqSourceFileRow :: FilePath -> (Int, ByteString) -> PoseidonIO (Either PoseidonException SeqSourceRow) Source #

A function to read one row of a seqSourceFile

warnSeqSourceConsistency :: FilePath -> SeqSourceRows -> PoseidonIO () Source #

checkRunsUnique :: SeqSourceRows -> Bool Source #

checkAtLeastOnePoseidonID :: SeqSourceRows -> Bool Source #