| Safe Haskell | Safe-Inferred |
|---|---|
| Language | Haskell2010 |
Poseidon.SequencingSource
Synopsis
- data AccessionID
- makeAccessionID :: MonadFail m => String -> m AccessionID
- newtype JURI = JURI String
- makeJURI :: MonadFail m => String -> m JURI
- data SSFUDG
- makeSSFUDG :: MonadFail m => String -> m SSFUDG
- data SSFLibraryBuilt
- makeSSFLibraryBuilt :: MonadFail m => String -> m SSFLibraryBuilt
- newtype SeqSourceRows = SeqSourceRows {}
- newtype AccessionIDRun = AccessionIDRun {}
- makeAccessionIDRun :: MonadFail m => String -> m AccessionIDRun
- newtype AccessionIDSample = AccessionIDSample {}
- makeAccessionIDSample :: MonadFail m => String -> m AccessionIDSample
- newtype AccessionIDStudy = AccessionIDStudy {}
- makeAccessionIDStudy :: MonadFail m => String -> m AccessionIDStudy
- newtype SimpleDate = SimpleDate Day
- makeSimpleDate :: MonadFail m => String -> m SimpleDate
- newtype MD5 = MD5 String
- makeMD5 :: MonadFail m => String -> m MD5
- isMD5Hash :: String -> Bool
- data SeqSourceRow = SeqSourceRow {
- sPoseidonID :: Maybe JannoStringList
- sUDG :: Maybe SSFUDG
- sLibraryBuilt :: Maybe SSFLibraryBuilt
- sSampleAccession :: Maybe AccessionIDSample
- sStudyAccession :: Maybe AccessionIDStudy
- sRunAccession :: Maybe AccessionIDRun
- sSampleAlias :: Maybe String
- sSecondarySampleAccession :: Maybe String
- sFirstPublic :: Maybe SimpleDate
- sLastUpdated :: Maybe SimpleDate
- sInstrumentModel :: Maybe String
- sLibraryLayout :: Maybe String
- sLibrarySource :: Maybe String
- sInstrumentPlatform :: Maybe String
- sLibraryName :: Maybe String
- sLibraryStrategy :: Maybe String
- sFastqFTP :: Maybe (ListColumn JURI)
- sFastqASPERA :: Maybe (ListColumn JURI)
- sFastqBytes :: Maybe (ListColumn Integer)
- sFastqMD5 :: Maybe (ListColumn MD5)
- sReadCount :: Maybe Integer
- sSubmittedFTP :: Maybe (ListColumn JURI)
- 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
data AccessionID Source #
A datatype to represent AccessionIDs in a ssf file
Constructors
| INSDCProject String | |
| INSDCStudy String | |
| INSDCBioSample String | |
| INSDCSample String | |
| INSDCExperiment String | |
| INSDCRun String | |
| INSDCAnalysis String | |
| OtherID String |
Instances
makeAccessionID :: MonadFail m => String -> m AccessionID Source #
A datatype to represent URIs in a ssf file
Instances
A datatype to represent UDG in a ssf file
Instances
| Bounded SSFUDG Source # | |
| Enum SSFUDG Source # | |
Defined in Poseidon.SequencingSource | |
| Generic SSFUDG Source # | |
| Show SSFUDG Source # | |
| FromField SSFUDG Source # | |
Defined in Poseidon.SequencingSource Methods parseField :: Field -> Parser SSFUDG | |
| ToField SSFUDG Source # | |
Defined in Poseidon.SequencingSource | |
| Eq SSFUDG Source # | |
| Ord SSFUDG Source # | |
| type Rep SSFUDG Source # | |
Defined in Poseidon.SequencingSource type Rep SSFUDG = D1 ('MetaData "SSFUDG" "Poseidon.SequencingSource" "poseidon-hs-1.6.0.0-CwGty8Kh6aTIT5Pu2ecao6" 'False) (C1 ('MetaCons "SSFMinus" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "SSFHalf" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "SSFPlus" 'PrefixI 'False) (U1 :: Type -> Type))) | |
data SSFLibraryBuilt Source #
A datatype to represent Library_Built in a janno file
Instances
makeSSFLibraryBuilt :: MonadFail m => String -> m SSFLibraryBuilt Source #
newtype SeqSourceRows Source #
A data type to represent a seqSourceFile
Constructors
| SeqSourceRows | |
Fields | |
Instances
newtype AccessionIDRun Source #
Constructors
| AccessionIDRun | |
Fields | |
Instances
makeAccessionIDRun :: MonadFail m => String -> m AccessionIDRun Source #
newtype AccessionIDSample Source #
Constructors
| AccessionIDSample | |
Fields | |
Instances
makeAccessionIDSample :: MonadFail m => String -> m AccessionIDSample Source #
newtype AccessionIDStudy Source #
Constructors
| AccessionIDStudy | |
Fields | |
Instances
makeAccessionIDStudy :: MonadFail m => String -> m AccessionIDStudy Source #
newtype SimpleDate Source #
A datatype for calendar dates
Constructors
| SimpleDate Day |
Instances
makeSimpleDate :: MonadFail m => String -> m SimpleDate Source #
A datatype to represent MD5 hashes
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
Instances
seqSourceHeader :: [ByteString] 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 #