Allow passing read name to mappy (#1260)

* Allow passing read name to mappy

This adds the (optional) ability to pass the read
name to the mappy `map` method.  Without the
read name, the call to `map` can sometimes give
different output than the command line version
of `minimap2` because of the way minimap uses
the hash of the read name to break ties in ordering
hits.  This can affect which / if certain
supplementary alignments are generated, and even
which / if non-primary alignments are generated.

* Pass name directly to mm_map_aux

Get rid of additional function, and always
accept the name parameter in the mm_map_aux
function (can be nullptr if not available).

---------

Co-authored-by: Rob Patro <rob@newton>

python/cmappy.h

@@ -71,13 +71,13 @@ static inline void mm_reset_timer(void)
 }
 
 extern unsigned char seq_comp_table[256];
-static inline mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char *seq1, const char *seq2, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt)
+static inline mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char* seqname, const char *seq1, const char *seq2, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt)
 {
 	mm_reg1_t *r;
 
 	Py_BEGIN_ALLOW_THREADS
 	if (seq2 == 0) {
-		r = mm_map(mi, strlen(seq1), seq1, n_regs, b, opt, NULL);
+		r = mm_map(mi, strlen(seq1), seq1, n_regs, b, opt, seqname);
 	} else {
 		int _n_regs[2];
 		mm_reg1_t *regs[2];
@@ -94,7 +94,7 @@ static inline mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char *seq1, const
 			seq[1][i] = seq_comp_table[t];
 		}
 		if (len[1]&1) seq[1][len[1]>>1] = seq_comp_table[(uint8_t)seq[1][len[1]>>1]];
-		mm_map_frag(mi, 2, len, (const char**)seq, _n_regs, regs, b, opt, NULL);
+		mm_map_frag(mi, 2, len, (const char**)seq, _n_regs, regs, b, opt, seqname);
 		for (i = 0; i < _n_regs[1]; ++i)
 			regs[1][i].rev = !regs[1][i].rev;
 		*n_regs = _n_regs[0] + _n_regs[1];

python/cmappy.pxd

@@ -129,7 +129,7 @@ cdef extern from "cmappy.h":
 
 	void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
 	void mm_free_reg1(mm_reg1_t *r)
-	mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char *seq1, const char *seq2, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt)
+	mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char* seqname, const char *seq1, const char *seq2, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt)
 	char *mappy_fetch_seq(const mm_idx_t *mi, const char *name, int st, int en, int *l)
 	mm_idx_t *mappy_idx_seq(int w, int k, int is_hpc, int bucket_bits, const char *seq, int l)
 

python/mappy.pyx

@@ -163,7 +163,7 @@ cdef class Aligner:
 	def __bool__(self):
 		return (self._idx != NULL)
 
-	def map(self, seq, seq2=None, buf=None, cs=False, MD=False, max_frag_len=None, extra_flags=None):
+	def map(self, seq, seq2=None, name=None, buf=None, cs=False, MD=False, max_frag_len=None, extra_flags=None):
 		cdef cmappy.mm_reg1_t *regs
 		cdef cmappy.mm_hitpy_t h
 		cdef ThreadBuffer b
@@ -185,11 +185,20 @@ cdef class Aligner:
 		km = cmappy.mm_tbuf_get_km(b._b)
 
 		_seq = seq if isinstance(seq, bytes) else seq.encode()
+		if name is not None:
+			_name = name if isinstance(name, bytes) else name.encode()
+
 		if seq2 is None:
-			regs = cmappy.mm_map_aux(self._idx, _seq, NULL,  &n_regs, b._b, &map_opt)
+			if name is None:
+				regs = cmappy.mm_map_aux(self._idx, NULL, _seq, NULL,  &n_regs, b._b, &map_opt)
+			else:
+				regs = cmappy.mm_map_aux(self._idx, _name, _seq, NULL,  &n_regs, b._b, &map_opt)
 		else:
 			_seq2 = seq2 if isinstance(seq2, bytes) else seq2.encode()
-			regs = cmappy.mm_map_aux(self._idx, _seq, _seq2, &n_regs, b._b, &map_opt)
+			if name is None:
+				regs = cmappy.mm_map_aux(self._idx, NULL, _seq, _seq2, &n_regs, b._b, &map_opt)
+			else:
+				regs = cmappy.mm_map_aux(self._idx, _name, _seq, _seq2, &n_regs, b._b, &map_opt)
 
 		try:
 			i = 0