first python version

python/cminimap2.h

@@ -0,0 +1,40 @@
+#ifndef CMINIMAP2_H
+#define CMINIMAP2_H
+
+#include <stdlib.h>
+#include "minimap.h"
+
+typedef struct {
+	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;
+
+static inline mm_hitpy_t *mm_reg2hitpy(const mm_idx_t *mi, int n_regs, mm_reg1_t *regs)
+{
+	mm_hitpy_t *h;
+	int i;
+	h = (mm_hitpy_t*)calloc(n_regs, sizeof(mm_hitpy_t));
+	for (i = 0; i < n_regs; ++i) {
+		mm_reg1_t *r = &regs[i];
+		h[i].ctg = mi->seq[r->rid].name;
+		h[i].ctg_start = r->rs, h[i].ctg_end = r->re;
+		h[i].qry_start = r->qs, h[i].qry_end = r->qe;
+		h[i].strand = r->rev;
+		h[i].mapq = r->mapq;
+		h[i].is_primary = (r->id == r->parent);
+		h[i].n_cigar32 = r->p->n_cigar;
+		h[i].cigar32 = r->p->cigar;
+	}
+	return h;
+}
+
+static inline void mm_free_reg1(mm_reg1_t *r)
+{
+	free(r->p);
+}
+
+#endif