updated mappy and example.c

example.c

@@ -43,8 +43,7 @@ int main(int argc, char *argv[])
 				mm_reg1_t *r = &reg[j];
 				assert(r->p); // with MM_F_CIGAR, this should not be NULL
 				printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
-				printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re,
+				printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re, r->mlen, r->blen, r->mapq);
-						r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen, r->mapq);
 				for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
 					printf("%d%c", r->p->cigar[i]>>4, "MIDSHN"[r->p->cigar[i]&0xf]);
 				putchar('\n');

python/README.rst

@@ -104,9 +104,13 @@ properties:
 
 * **mapq**: mapping quality
 
-* **NM**: number of mismatches and gaps in the alignment
-
 * **blen**: length of the alignment, including both alignment matches and gaps
+  but excluding ambiguous bases.
+
+* **mlen**: length of the matching bases in the alignment, excluding ambiguous
+  base matches.
+
+* **NM**: number of mismatches, gaps and ambiguous poistions in the alignment
 
 * **trans_strand**: transcript strand. +1 if on the forward strand; -1 if on the
   reverse strand; 0 if unknown
@@ -124,7 +128,7 @@ the following format:
 
 ::
 
-	q_st  q_en  strand  ctg  ctg_len  r_st  r_en  blen-NM  blen  mapq  cg:Z:cigar_str
+	q_st  q_en  strand  ctg  ctg_len  r_st  r_en  mlen  blen  mapq  cg:Z:cigar_str
 
 It is effectively the PAF format without the QueryName and QueryLength columns
 (the first two columns in PAF).

python/cmappy.h

@@ -12,7 +12,7 @@ typedef struct {
 	const char *ctg;
 	int32_t ctg_start, ctg_end;
 	int32_t qry_start, qry_end;
-	int32_t blen, NM, ctg_len;
+	int32_t blen, mlen, NM, ctg_len;
 	uint8_t mapq, is_primary;
 	int8_t strand, trans_strand;
 	int32_t n_cigar32;
@@ -27,8 +27,9 @@ static inline void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
 	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->mlen = r->mlen;
-	h->NM = r->p->n_diff;
+	h->blen = r->blen;
+	h->NM = r->blen - r->mlen + r->p->n_ambi;
 	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;

python/cmappy.pxd

@@ -15,17 +15,20 @@ cdef extern from "minimap.h":
 		int flag
 		int bw
 		int max_gap, max_gap_ref
+		int max_frag_len
 		int max_chain_skip
 		int min_cnt
 		int min_chain_score
 		float mask_level
 		float pri_ratio
 		int best_n
+		float min_iden
 		int max_join_long, max_join_short
 		int min_join_flank_sc
 		int a, b, q, e, q2, e2
 		int noncan
 		int zdrop
+		int end_bonus
 		int min_dp_max
 		int min_ksw_len
 		int pe_ori, pe_bonus
@@ -86,7 +89,7 @@ cdef extern from "cmappy.h":
 		const char *ctg
 		int32_t ctg_start, ctg_end
 		int32_t qry_start, qry_end
-		int32_t blen, NM, ctg_len
+		int32_t blen, mlen, NM, ctg_len
 		uint8_t mapq, is_primary
 		int8_t strand, trans_strand
 		int32_t n_cigar32

python/mappy.pyx

@@ -7,15 +7,15 @@ cmappy.mm_reset_timer()
 cdef class Alignment:
 	cdef int _ctg_len, _r_st, _r_en
 	cdef int _q_st, _q_en
-	cdef int _NM, _blen
+	cdef int _NM, _mlen, _blen
 	cdef int8_t _strand, _trans_strand
 	cdef uint8_t _mapq, _is_primary
 	cdef _ctg, _cigar # these are python objects
 
-	def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, blen, NM, trans_strand):
+	def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, mlen, blen, NM, trans_strand):
 		self._ctg, self._ctg_len, self._r_st, self._r_en = str(ctg), cl, cs, ce
 		self._strand, self._q_st, self._q_en = strand, qs, qe
-		self._NM, self._blen = NM, blen
+		self._NM, self._mlen, self._blen = NM, mlen, blen
 		self._mapq = mapq
 		self._cigar = cigar
 		self._is_primary = is_primary
@@ -39,6 +39,12 @@ cdef class Alignment:
 	@property
 	def trans_strand(self): return self._trans_strand
 
+	@property
+	def blen(self): return self._blen
+
+	@property
+	def mlen(self): return self._mlen
+
 	@property
 	def NM(self): return self._NM
 
@@ -71,7 +77,7 @@ cdef class Alignment:
 		elif self._trans_strand < 0: ts = 'ts:A:-'
 		else: ts = 'ts:A:.'
 		return "\t".join([str(self._q_st), str(self._q_en), strand, self._ctg, str(self._ctg_len), str(self._r_st), str(self._r_en),
-				str(self._blen - self._NM), str(self._blen), str(self._mapq), tp, ts, "cg:Z:" + self.cigar_str])
+				str(self._mlen), str(self._blen), str(self._mapq), tp, ts, "cg:Z:" + self.cigar_str])
 
 cdef class ThreadBuffer:
 	cdef cmappy.mm_tbuf_t *_b
@@ -135,7 +141,7 @@ cdef class Aligner:
 			for k in range(h.n_cigar32):
 				c = h.cigar32[k]
 				cigar.append([c>>4, c&0xf])
-			yield Alignment(h.ctg, h.ctg_len, h.ctg_start, h.ctg_end, h.strand, h.qry_start, h.qry_end, h.mapq, cigar, h.is_primary, h.blen, h.NM, h.trans_strand)
+			yield Alignment(h.ctg, h.ctg_len, h.ctg_start, h.ctg_end, h.strand, h.qry_start, h.qry_end, h.mapq, cigar, h.is_primary, h.mlen, h.blen, h.NM, h.trans_strand)
 			cmappy.mm_free_reg1(&regs[i])
 		free(regs)
 

setup.py

@@ -33,7 +33,7 @@ setup(
 	keywords = 'sequence-alignment',
 	scripts = ['python/minimap2.py'],
     ext_modules = [Extension('mappy',
-		sources = [module_src, 'align.c', 'bseq.c', 'chain.c', 'format.c', 'hit.c', 'index.c',
+		sources = [module_src, 'align.c', 'bseq.c', 'chain.c', 'format.c', 'hit.c', 'index.c', 'pe.c',
 				   'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
 				   'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c'],
 		depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',