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r436: working on short reads 

The result is mixed - lots of room for tuning
This commit is contained in:
Heng Li 2017-09-25 14:06:29 -04:00
parent 3bb66e1ed3
commit 81008dd371
2 changed files with 16 additions and 11 deletions
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26
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r424-dirty"
#define MM_VERSION "2.2-r436-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -37,9 +37,8 @@ static struct option long_options[] = {
{ "cost-non-gt-ag", required_argument, 0, 0 },
{ "no-sam-sq", no_argument, 0, 0 },
{ "sr", no_argument, 0, 0 },
{ "multi-segment", no_argument, 0, 0 },
{ "2nd-seg-rev", no_argument, 0, 0 },
{ "2nd-seg-for", no_argument, 0, 0 },
{ "multi-seg", optional_argument, 0, 0 },
{ "2nd-seg-rev", optional_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@ -118,10 +117,15 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_SAM_SQ; // --no-sam-sq
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
else if (c == 0 && long_idx ==14) opt.flag |= MM_F_MULTI_SEG; // --multi-seg
else if (c == 0 && long_idx ==15) opt.flag |= MM_F_SEG_REV; // --2nd-seg-rev
else if (c == 0 && long_idx ==16) opt.flag &= ~MM_F_SEG_REV; // --2nd-seg-for
else if (c == 'V') {
else if (c == 0 && long_idx ==14) { // --multi-seg
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag |= MM_F_MULTI_SEG;
else opt.flag &= ~MM_F_MULTI_SEG;
} else if (c == 0 && long_idx ==15) { // --2nd-seg-rev
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag |= MM_F_SEG_REV;
else opt.flag &= ~MM_F_SEG_REV;
} else if (c == 'V') {
puts(MM_VERSION);
return 0;
} else if (c == 'f') {
@ -165,15 +169,15 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -d FILE dump index to FILE []\n");
fprintf(fp_help, " Mapping:\n");
fprintf(fp_help, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac);
fprintf(fp_help, " -g INT stop chain enlongation if there are no minimizers in INT-bp [%d]\n", opt.max_gap);
fprintf(fp_help, " -r INT bandwidth used in chaining and DP-based alignment [%d]\n", opt.bw);
fprintf(fp_help, " -g NUM stop chain enlongation if there are no minimizers in INT-bp [%d]\n", opt.max_gap);
fprintf(fp_help, " -G NUM max intron length (-x splice) [200k]; or insert size (-x sr) [1000] []\n");
fprintf(fp_help, " -r NUM bandwidth used in chaining and DP-based alignment [%d]\n", opt.bw);
fprintf(fp_help, " -n INT minimal number of minimizers on a chain [%d]\n", opt.min_cnt);
fprintf(fp_help, " -m INT minimal chaining score (matching bases minus log gap penalty) [%d]\n", opt.min_chain_score);
// fprintf(fp_help, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); // TODO: this option is never used; might be buggy
fprintf(fp_help, " -X skip self and dual mappings (for the all-vs-all mode)\n");
fprintf(fp_help, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
fprintf(fp_help, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n);
fprintf(fp_help, " -G NUM max intron length (only effective following -x splice) [200k]\n");
fprintf(fp_help, " Alignment:\n");
fprintf(fp_help, " -A INT matching score [%d]\n", opt.a);
fprintf(fp_help, " -B INT mismatch penalty [%d]\n", opt.b);

1
map.c
View File

@ -78,6 +78,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->flag |= MM_F_SR | MM_F_MULTI_SEG | MM_F_SEG_REV;
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1;
mo->max_gap = 100;
mo->max_gap_ref = 1000;
mo->pri_ratio = 0.5f;
mo->min_cnt = 2;
mo->min_chain_score = 20;