renamed module name from minimap2 to mmappy

minimap2 clashed with minimap2 from conda

python/cmmappy.h

@@ -0,0 +1,39 @@
+#ifndef CMMAPPY_H
+#define CMMAPPY_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 blen, NM, ctg_len;
+	uint8_t mapq, is_primary;
+	int8_t strand, trans_strand;
+	int32_t n_cigar32;
+	uint32_t *cigar32;
+} mm_hitpy_t;
+
+static inline void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
+{
+	h->ctg = mi->seq[r->rid].name;
+	h->ctg_len = mi->seq[r->rid].len;
+	h->ctg_start = r->rs, h->ctg_end = r->re;
+	h->qry_start = r->qs, h->qry_end = r->qe;
+	h->strand = r->rev? -1 : 1;
+	h->mapq = r->mapq;
+	h->blen = r->p->blen;
+	h->NM = r->p->n_diff;
+	h->trans_strand = r->p->trans_strand == 1? 1 : r->p->trans_strand == 2? -1 : 0;
+	h->is_primary = (r->id == r->parent);
+	h->n_cigar32 = r->p->n_cigar;
+	h->cigar32 = r->p->cigar;
+}
+
+static inline void mm_free_reg1(mm_reg1_t *r)
+{
+	free(r->p);
+}
+
+#endif