first python version

python/cminimap2.pxd

@@ -0,0 +1,87 @@
+from libc.stdint cimport uint8_t, int32_t, int64_t, uint32_t, uint64_t
+
+cdef extern from "minimap.h":
+	#
+	# Options
+	#
+	ctypedef struct mm_idxopt_t:
+		short k, w, is_hpc, bucket_bits
+		int mini_batch_size
+		uint64_t batch_size
+
+	ctypedef struct mm_mapopt_t:
+		int sdust_thres
+		int flag
+		int bw
+		int max_gap, max_gap_ref
+		int max_chain_skip
+		int min_cnt
+		int min_chain_score
+		float mask_level
+		float pri_ratio
+		int best_n
+		int max_join_long, max_join_short
+		int min_join_flank_sc
+		int a, b, q, e, q2, e2
+		int noncan
+		int zdrop
+		int min_dp_max
+		int min_ksw_len
+		float mid_occ_frac
+		int32_t mid_occ
+		int mini_batch_size
+
+	int mm_set_opt(char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
+
+	#
+	# Indexing
+	#
+	ctypedef struct mm_idx_seq_t:
+		char *name
+		uint64_t offset
+		uint32_t len
+
+	ctypedef struct mm_idx_bucket_t:
+		pass
+
+	ctypedef struct mm_idx_t:
+		int32_t b, w, k, is_hpc
+		uint32_t n_seq
+		mm_idx_seq_t *seq
+		uint32_t *S
+		mm_idx_bucket_t *B
+		void *km
+
+	ctypedef struct mm_idx_reader_t:
+		pass
+
+	mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt, const char *fn_out)
+	mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
+	void mm_idx_reader_close(mm_idx_reader_t *r)
+	void mm_idx_destroy(mm_idx_t *mi)
+	void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
+
+	#
+	# Mapping (key struct defined in cminimap2.h below)
+	#
+	ctypedef struct mm_reg1_t:
+		pass
+
+	ctypedef struct mm_tbuf_t:
+		pass
+
+	mm_tbuf_t *mm_tbuf_init()
+	void mm_tbuf_destroy(mm_tbuf_t *b)
+	mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name)
+
+cdef extern from "cminimap2.h":
+	ctypedef struct mm_hitpy_t:
+		const char *ctg
+		int32_t ctg_start, ctg_end
+		int32_t qry_start, qry_end
+		int32_t n_cigar32
+		uint8_t strand, mapq, is_primary
+		uint32_t *cigar32
+	
+	mm_hitpy_t *mm_reg2hitpy(const mm_idx_t *mi, int n_regs, mm_reg1_t *regs)
+	void mm_free_reg1(mm_reg1_t *r)