bio-0.4.6: A bioinformatics library Source code Contents Index

Bio.Alignment.Soap

Synopsis

data SoapAlign = SA { name :: !SeqName sequ :: !SeqData qual :: !QualData nhit :: !Int pairend :: !Char length :: !Offset strand :: !Strand refname :: !SeqName refstart :: !Offset nmismatch :: !Int mismatches :: ![SoapAlignMismatch] } data SoapAlignMismatch = SAM { readnt :: !Char refnt :: !Char offset :: !Offset qualnt :: !Qual } refSeqPos :: SoapAlign -> SeqPos refCSeqLoc :: SoapAlign -> ContigSeqLoc refSeqLoc :: SoapAlign -> SeqLoc mismatchSeqPos :: SoapAlign -> SoapAlignMismatch -> SeqPos parse :: (Error e, MonadError e m) => ByteString -> m SoapAlign unparse :: SoapAlign -> ByteString parseMismatch :: (Error e, MonadError e m) => ByteString -> m SoapAlignMismatch unparseMismatch :: SoapAlignMismatch -> ByteString group :: [SoapAlign] -> [[SoapAlign]]

Documentation

data SoapAlign Source

Alignment output from SOAP Constructors SA name :: !SeqName sequ :: !SeqData Reference strand orientation sequence qual :: !QualData Reference strand orientation quality data nhit :: !Int pairend :: !Char length :: !Offset strand :: !Strand refname :: !SeqName refstart :: !Offset 1-based index, as output by SOAP, of reference strand 5' end nmismatch :: !Int mismatches :: ![SoapAlignMismatch] Instances Eq SoapAlign Ord SoapAlign Read SoapAlign Show SoapAlign

data SoapAlignMismatch Source

Constructors SAM readnt :: !Char Read nt in reference strand orientation refnt :: !Char Reference nt in reference strand orientation offset :: !Offset Offset from reference strand 5' end in reference strand orientation qualnt :: !Qual Quality score of read nt Instances Eq SoapAlignMismatch Ord SoapAlignMismatch Read SoapAlignMismatch Show SoapAlignMismatch

refSeqPos :: SoapAlign -> SeqPos Source

refCSeqLoc :: SoapAlign -> ContigSeqLoc Source

refSeqLoc :: SoapAlign -> SeqLoc Source

mismatchSeqPos :: SoapAlign -> SoapAlignMismatch -> SeqPos Source

parse :: (Error e, MonadError e m) => ByteString -> m SoapAlign Source

unparse :: SoapAlign -> ByteString Source

parseMismatch :: (Error e, MonadError e m) => ByteString -> m SoapAlignMismatch Source

unparseMismatch :: SoapAlignMismatch -> ByteString Source

group :: [SoapAlign] -> [[SoapAlign]] Source

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