Safe Haskell | Safe-Infered |
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Handling of the extended CIGAR pair-wise alignment descriptors
Documentation
Cigar entry types
Match | Aligned nucleotide, may be a match or mismatch |
Ins | Insertion in read relative to reference |
Del | Deletion from read relative to reference |
RefSkip | Skipped reference bases, i.e., splice |
SoftClip | Trimmed nucleotides, still present in read |
HardClip | Trimmed nucleotides, removed from read |
Pad | Deletion from padded reference |
Cigar entry including length
cigarToSpLoc :: Int64 -> [Cigar] -> SpliceLocSource