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from libc.stdint cimport int8_t, uint8_t, int32_t, int64_t, uint32_t, uint64_t
from libc.stdio cimport FILE
cdef extern from "simd_instruction.h":
int simd_check()
cdef extern from "abpoa.h":
cdef int ABPOA_GLOBAL_MODE "ABPOA_GLOBAL_MODE"
cdef int ABPOA_LOCAL_MODE "ABPOA_LOCAL_MODE"
cdef int ABPOA_EXTEND_MODE "ABPOA_EXTEND_MODE"
# gap mode
cdef int ABPOA_LINEAR_GAP "ABPOA_LINEAR_GAP"
cdef int ABPOA_AFFINE_GAP "ABPOA_AFFINE_GAP"
cdef int ABPOA_CONVEX_GAP "ABPOA_CONVEX_GAP"
cdef int ABPOA_EXTRA_B "ABPOA_EXTRA_B"
cdef float ABPOA_EXTRA_F "ABPOA_EXTRA_F"
cdef char *ABPOA_CIGAR_STR "ABPOA_CIGAR_STR"
cdef int ABPOA_CMATCH "ABPOA_CMATCH"
cdef int ABPOA_CINS "ABPOA_CINS"
cdef int ABPOA_CDEL "ABPOA_CDEL"
cdef int ABPOA_CDIFF "ABPOA_CDIFF"
cdef int ABPOA_CSOFT_CLIP "ABPOA_CSOFT_CLIP"
cdef int ABPOA_CHARD_CLIP "ABPOA_CHARD_CLIP"
cdef int ABPOA_SRC_NODE_ID "ABPOA_SRC_NODE_ID"
cdef int ABPOA_SINK_NODE_ID "ABPOA_SINK_NODE_ID"
cdef int ABPOA_OUT_CONS "ABPOA_OUT_CONS"
cdef int ABPOA_OUT_MSA "ABPOA_OUT_MSA"
cdef int ABPOA_OUT_CONS_MSA "ABPOA_OUT_CONS_MSA"
cdef int ABPOA_OUT_GFA "ABPOA_OUT_GFA"
cdef int ABPOA_OUT_CONS_GFA "ABPOA_OUT_CONS_GFA"
cdef int ABPOA_HB "ABPOA_HB"
cdef int ABPOA_MF "ABPOA_MF"
ctypedef struct abpoa_res_t:
int n_cigar, m_cigar
uint64_t *graph_cigar
int node_s, node_e, query_s, query_e # for local and extension mode
int n_aln_bases, n_matched_bases
uint32_t best_score
ctypedef struct abpoa_para_t:
int m
int *mat # score matrix
char *mat_fn
int use_score_matrix
int match, max_mat, mismatch, min_mis, gap_open1, gap_open2, gap_ext1, gap_ext2
int inf_min
int k, w, min_w
int wb # 1st part of extra band width
float wf # 2nd part of extra band width. w=wb+wf*L (L is sequence length)
int zdrop, end_bonus # from minimap2
# int simd_flag # available SIMD instruction
# alignment mode
uint8_t ret_cigar, rev_cigar, out_msa, out_cons, out_gfa, out_fq, use_read_ids, amb_strand # mode: 0: global, 1: local, 2: extend
uint8_t sub_aln, use_qv, disable_seeding, progressive_poa
char *incr_fn
char *out_pog
int align_mode, gap_mode, max_n_cons, cons_algrm
double min_freq # for diploid data
int verbose
ctypedef struct abpoa_node_t:
int node_id
int in_edge_n, in_edge_m
int *in_id
int out_edge_n, out_edge_m
int *out_id
int *out_weight
int *read_weight
int n_read, m_read, n_span_read
uint64_t **read_ids
int read_ids_n # for diploid
int aligned_node_n, aligned_node_m
int *aligned_node_id # mismatch; aligned node will have same rank
uint8_t base # 0~m
ctypedef struct abpoa_graph_t:
abpoa_node_t *node
int node_n, node_m, index_rank_m
int *index_to_node_id
int *node_id_to_index
int *node_id_to_max_pos_left
int *node_id_to_max_pos_right
int *node_id_to_max_remain
int *node_id_to_msa_rank
uint8_t is_topological_sorted, is_called_cons, is_set_msa_rank
ctypedef struct abpoa_cons_t:
int n_cons, n_seq, msa_len
int *clu_n_seq
int **clu_read_ids
int *cons_len
int **cons_node_ids
uint8_t **cons_base
uint8_t **msa_base
int **cons_cov
int **cons_phred_score;
ctypedef struct abpoa_str_t:
int l, m
char *s
ctypedef struct abpoa_seq_t:
int n_seq, m_seq
abpoa_str_t *seq
abpoa_str_t *name
abpoa_str_t *comment
abpoa_str_t *qual
uint8_t *is_rc
ctypedef struct abpoa_simd_matrix_t:
pass
ctypedef struct abpoa_t:
abpoa_graph_t *abg
abpoa_seq_t *abs
abpoa_simd_matrix_t *abm
abpoa_cons_t *abc
# init for abpoa parameters
abpoa_para_t *abpoa_init_para()
void abpoa_set_mat_from_file(abpoa_para_t *abpt, char *mtx_fn)
void abpoa_post_set_para(abpoa_para_t *abpt)
void abpoa_free_para(abpoa_para_t *abpt)
# init for alignment
abpoa_t *abpoa_init()
void abpoa_free(abpoa_t *ab)
# do msa for a set of input sequences
int abpoa_msa(abpoa_t *ab, abpoa_para_t *abpt, int n_seqs, char **seq_names, int *seq_lens, uint8_t **seqs, int ** qual_weights, FILE *out_fp)
int abpoa_msa1(abpoa_t *ab, abpoa_para_t *abpt, char *read_fn, FILE *out_fp)
# clean alignment graph
void abpoa_reset(abpoa_t *ab, abpoa_para_t *abpt, int qlen)
# restore graph from GFA/MSA file
abpoa_t *abpoa_restore_graph(abpoa_t *ab, abpoa_para_t *abpt)
# align a sequence to a graph
int abpoa_align_sequence_to_graph(abpoa_t *ab, abpoa_para_t *abpt, uint8_t *query, int qlen, abpoa_res_t *res)
# align to sub-graph
void abpoa_subgraph_nodes(abpoa_t *ab, abpoa_para_t *abpt, int inc_beg, int inc_end, int *exc_beg, int *exc_end)
int abpoa_align_sequence_to_subgraph(abpoa_t *ab, abpoa_para_t *abpt, int beg_node_id, int end_node_id, uint8_t *query, int qlen, abpoa_res_t *res)
# add an alignment to a graph
int abpoa_add_graph_node(abpoa_graph_t *abg, uint8_t base)
void abpoa_add_graph_edge(abpoa_graph_t *abg, int from_id, int to_id, int check_edge, int w, uint8_t add_read_id, uint8_t add_read_weight, int read_id, int read_ids_n, int tot_read_n)
int abpoa_add_graph_alignment(abpoa_t *ab, abpoa_para_t *abpt, uint8_t *query, int *weight, int qlen, int *qpos_to_node_id, abpoa_res_t res, int read_id, int tot_read_n, int inc_both_ends)
int abpoa_add_subgraph_alignment(abpoa_t *ab, abpoa_para_t *abpt, int beg_node_id, int end_node_id, uint8_t *query, int *weight, int qlen, int *qpos_to_node_id, abpoa_res_t res, int read_id, int tot_read_n, int inc_both_ends)
void abpoa_BFS_set_node_index(abpoa_graph_t *abg, int src_id, int sink_id)
void abpoa_BFS_set_node_remain(abpoa_graph_t *abg, int src_id, int sink_id)
void abpoa_topological_sort(abpoa_graph_t *abg, abpoa_para_t *abpt)
# generate consensus sequence from graph
# para:
# out_fp: consensus sequence output in FASTA format, set as NULL to disable
void abpoa_generate_consensus(abpoa_t *ab, abpoa_para_t *abpt)
void abpoa_output_fx_consensus(abpoa_t *ab, abpoa_para_t *abpt, FILE *out_fp)
# generate column multiple sequence alignment from graph
void abpoa_generate_rc_msa(abpoa_t *ab, abpoa_para_t *abpt)
void abpoa_output_rc_msa(abpoa_t *ab, abpoa_para_t *abpt, FILE *out_fp)
# generate full graph in GFA format
void abpoa_generate_gfa(abpoa_t *ab, abpoa_para_t *abpt, FILE *out_fp)
# output to out_fp
void abpoa_output(abpoa_t *ab, abpoa_para_t *abpt, FILE *out_fp)
# generate DOT graph plot
void abpoa_dump_pog(abpoa_t *ab, abpoa_para_t *abpt)
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