| bio-0.4: 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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