| 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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