Improving 'properly paired' flag.

If one end has a low quality tail that happens to have a score-20 hit,
the pair won't be flagged as properly paired because bwa-mem thought it has
multiple hits. By filtering with -T, we won't have this problem.

bwa.1

@@ -235,7 +235,7 @@ attached to every read in the output. An example is '@RG\\tID:foo\\tSM:bar'.
 .BI -T \ INT
 Don't output alignment with score lower than
 .IR INT .
-This option only affects output. [30]
+This option affects output and occasionally SAM flag 2. [30]
 .TP
 .B -a
 Output all found alignments for single-end or unpaired paired-end reads. These

bwamem_pair.c

@@ -260,7 +260,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 		// 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)
-				if (a[i].a[j].secondary < 0) break;
+				if (a[i].a[j].secondary < 0 && a[i].a[j].score >= opt->T) break;
 			is_multi[i] = j < a[i].n? 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

main.c

@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.1-r347"
+#define PACKAGE_VERSION "0.7.1-r348-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);