r826: improved alt mapping for PE

bwamem_pair.c

@@ -276,9 +276,9 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 		char **XA[2];
 		// check if an end has multiple hits even after mate-SW
 		for (i = 0; i < 2; ++i) {
-			for (j = 1; j < a[i].n; ++j)
+			for (j = 1; j < n_pri[i]; ++j)
 				if (a[i].a[j].secondary < 0 && a[i].a[j].score >= opt->T) break;
-			is_multi[i] = j < a[i].n? 1 : 0;
+			is_multi[i] = j < n_pri[i]? 1 : 0;
 		}
 		if (is_multi[0] || is_multi[1]) goto no_pairing; // TODO: in rare cases, the true hit may be long but with low score
 		// compute mapQ for the best SE hit
@@ -316,7 +316,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 				int k = a[i].a[z[i]].secondary;
 				if (k >= 0) { // switch secondary and primary
 					assert(a[i].a[k].secondary < 0);
-					for (j = 0; j < a[i].n; ++j)
+					for (j = 0; j < n_pri[i]; ++j)
 						if (a[i].a[j].secondary == k || j == k)
 							a[i].a[j].secondary = z[i];
 					a[i].a[z[i]].secondary = -1;

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r824-dirty"
+#define PACKAGE_VERSION "0.7.10-r826-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);