From ce026a07fc8f01a1e45c86fdd40acf6843c378ac Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 19 Feb 2014 13:10:33 -0500 Subject: [PATCH] r439: expose mem_opt_t::max_matesw --- README.md | 3 ++- fastmap.c | 4 +++- main.c | 2 +- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 009a4ca..ac1e57e 100644 --- a/README.md +++ b/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 diff --git a/fastmap.c b/fastmap.c index 40cea8c..72d850c 100644 --- a/fastmap.c +++ b/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); diff --git a/main.c b/main.c index 5006f99..c264abe 100644 --- a/main.c +++ b/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[]);