r439: expose mem_opt_t::max_matesw

README.md

@@ -26,7 +26,7 @@ different sub-commands: **aln/samse/sampe** for BWA-backtrack,
 ###Availability
 
 BWA is released under [GPLv3][1]. The latest souce code is [freely
-available][2] at github. Released packages can [be downloaded ][3] at
+available][2] at github. Released packages can [be downloaded][3] at
 SourceForge. After you acquire the source code, simply use `make` to compile
 and copy the single executable `bwa` to the destination you want. The only
 dependency of BWA is [zlib][14].
@@ -73,3 +73,4 @@ do not have plan to submit it to a peer-reviewed journal in the near future.
 [12]: http://arxiv.org/abs/1303.3997
 [13]: http://arxiv.org/
 [14]: http://zlib.net/
+[15]: https://github.com/lh3/bwa/tree/mem

fastmap.c

@@ -30,7 +30,7 @@ int main_mem(int argc, char *argv[])
 	int64_t n_processed = 0;
 
 	opt = mem_opt_init();
-	while ((c = getopt(argc, argv, "paMCSPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:")) >= 0) {
+	while ((c = getopt(argc, argv, "paMCSPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg);
 		else if (c == 'w') opt->w = atoi(optarg);
 		else if (c == 'A') opt->a = atoi(optarg);
@@ -50,6 +50,7 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'v') bwa_verbose = atoi(optarg);
 		else if (c == 'r') opt->split_factor = atof(optarg);
 		else if (c == 'D') opt->chain_drop_ratio = atof(optarg);
+		else if (c == 'm') opt->max_matesw = atoi(optarg);
 		else if (c == 'C') copy_comment = 1;
 		else if (c == 'Q') {
 			opt->mapQ_coef_len = atoi(optarg);
@@ -77,6 +78,7 @@ int main_mem(int argc, char *argv[])
 //		fprintf(stderr, "       -s INT     look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
 		fprintf(stderr, "       -c INT     skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
 		fprintf(stderr, "       -D FLOAT   drop chains shorter than FLOAT fraction of the longest overlapping chain [%.2f]\n", opt->chain_drop_ratio);
+		fprintf(stderr, "       -m INT     perform at most INT rounds of mate rescues for each read [%d]\n", opt->max_matesw);
 		fprintf(stderr, "       -S         skip mate rescue\n");
 		fprintf(stderr, "       -P         skip pairing; mate rescue performed unless -S also in use\n");
 		fprintf(stderr, "       -A INT     score for a sequence match [%d]\n", opt->a);

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.6a+dev-r438"
+#define PACKAGE_VERSION "0.7.6a+dev-r439"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);