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r439: expose mem_opt_t::max_matesw

This commit is contained in:
Heng Li 2014-02-19 13:10:33 -05:00
parent 17fb85a227
commit ce026a07fc
3 changed files with 6 additions and 3 deletions
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3
README.md
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@ -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

4
fastmap.c
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@ -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);

2
main.c
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@ -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[]);