r436: fix rare MD/NM-CIGAR inconsistencies

bwa.c

@@ -125,14 +125,15 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
 		// NW alignment
 		*score = ksw_global(l_query, query, rlen, rseq, 5, mat, q, r, w, n_cigar, &cigar);
 	}
-	{// compute NM
+	{// compute NM and MD
 		int k, x, y, u, n_mm = 0, n_gap = 0;
 		str.l = str.m = *n_cigar * 4; str.s = (char*)cigar; // append MD to CIGAR
 		int2base = rb < l_pac? "ACGTN" : "TGCAN";
 		for (k = 0, x = y = u = 0; k < *n_cigar; ++k) {
 			int op, len;
 			cigar = (uint32_t*)str.s;
 			op  = cigar[k]&0xf, len = cigar[k]>>4;
+			if (op == 2 && (k == 0 || k == *n_cigar - 1)) continue; // skip the leading or trailing deletions
 			if (op == 0) { // match
 				for (i = 0; i < len; ++i) {
 					if (query[x + i] != rseq[y + i]) {

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.6a+dev-r435"
+#define PACKAGE_VERSION "0.7.6a+dev-r436"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);