bio-0.5.3: A bioinformatics library

Safe HaskellSafe-Inferred

Bio.Alignment.Soap

Synopsis

Documentation

data SoapAlign Source

Alignment output from SOAP

Constructors

SA 

Fields

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]
 

data SoapAlignMismatch Source

Constructors

SAM 

Fields

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