dev-r1079: per-read error rate

more tuning needed

minimap.h

@@ -147,7 +147,6 @@ typedef struct {
 	float alt_drop;
 
 	int a, b, q, e, q2, e2; // matching score, mismatch, gap-open and gap-ext penalties
-	int b2; // used for re-ranking hits
 	int sc_ambi; // score when one or both bases are "N"
 	int noncan;      // cost of non-canonical splicing sites
 	int junc_bonus;
@@ -158,6 +157,9 @@ typedef struct {
 	int anchor_ext_len, anchor_ext_shift;
 	float max_clip_ratio; // drop an alignment if BOTH ends are clipped above this ratio
 
+	int rank_min_len;
+	float rank_frac;
+
 	int pe_ori, pe_bonus;
 
 	float mid_occ_frac;  // only used by mm_mapopt_update(); see below