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module Bio.Alignment.Pairwise where
import Data.BitVector
import Data.Matrix
import Control.DeepSeq
import Numeric.LogDouble
data PairHMM
foreign import bpcall "Alignment:" transition_counts :: PairwiseAlignment -> Matrix Int
foreign import bpcall "Alignment:" pairwise_alignment_probability_from_counts :: Matrix Int -> PairHMM -> LogDouble
data PairwiseAlignment = PairwiseAlignment
foreign import bpcall "Alignment:" numInsert :: PairwiseAlignment -> Int
foreign import bpcall "Alignment:" numMatch :: PairwiseAlignment -> Int
foreign import bpcall "Alignment:" numDelete :: PairwiseAlignment -> Int
foreign import bpcall "Alignment:" numIndels :: PairwiseAlignment -> Int
foreign import bpcall "Alignment:" lengthIndels :: PairwiseAlignment -> Int
foreign import bpcall "Alignment:pairwise_alignment_length1" pairwise_alignment_length1 :: PairwiseAlignment -> Int
foreign import bpcall "Alignment:pairwise_alignment_length2" pairwise_alignment_length2 :: PairwiseAlignment -> Int
foreign import bpcall "Bits:pairwise_alignment_from_bits" builtin_pairwise_alignment_from_bits :: CBitVector -> CBitVector -> PairwiseAlignment
pairwise_alignment_from_bits :: BitVector -> BitVector -> PairwiseAlignment
pairwise_alignment_from_bits (BitVector x) (BitVector y) = builtin_pairwise_alignment_from_bits x y
foreign import bpcall "Alignment:unaligned_pairwise_alignment" unaligned_pairwise_alignment :: Int -> Int -> PairwiseAlignment
foreign import bpcall "Alignment:left_aligned_pairwise_alignment" left_aligned_pairwise_alignment :: Int -> Int -> PairwiseAlignment
foreign import bpcall "Alignment:flip_alignment" flip_alignment :: PairwiseAlignment -> PairwiseAlignment
instance NFData PairHMM
instance NFData PairwiseAlignment
foreign import bpcall "Alignment:" showPairwiseAlignmentRaw :: PairwiseAlignment -> CPPString
instance Show PairwiseAlignment where
show = unpack_cpp_string . showPairwiseAlignmentRaw
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