@param ref Reference sequence
@param l_ref Length of reference
@param query Query sequence
@param l_query Length of query sequence
@param iqual Query base qualities
@param c Alignment parameters
@paramout state Output alignment
@paramout q Phred scaled posterior probability of statei being wrong
@return Phred-scaled likelihood score, or INT_MIN on failure.
The reference and query sequences are coded using integers 0,1,2,3,4 for
bases A,C,G,T,N respectively (N here is for any ambiguity code).
On output, state and q are arrays of length l_query. The higher 30
bits give the reference position the query base is matched to and the
lower two bits can be 0 (an alignment match) or 1 (an
insertion). qi gives the phred scaled posterior probability of
statei being wrong.
On failure, errno will be set to EINVAL if the values of l_ref or l_query
were invalid; or ENOMEM if a memory allocation failed.
@param ref Reference sequence @param l_ref Length of reference @param query Query sequence @param l_query Length of query sequence @param iqual Query base qualities @param c Alignment parameters @paramout state Output alignment @paramout q Phred scaled posterior probability of statei being wrong @return Phred-scaled likelihood score, or INT_MIN on failure.
The reference and query sequences are coded using integers 0,1,2,3,4 for bases A,C,G,T,N respectively (N here is for any ambiguity code).
On output, state and q are arrays of length l_query. The higher 30 bits give the reference position the query base is matched to and the lower two bits can be 0 (an alignment match) or 1 (an insertion). qi gives the phred scaled posterior probability of statei being wrong.
On failure, errno will be set to EINVAL if the values of l_ref or l_query were invalid; or ENOMEM if a memory allocation failed.