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r365: documented the "sr" preset

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Heng Li
2017-09-14 12:57:21 -04:00
parent 4d3768bf26
commit 0f7455cefa
4 changed files with 14 additions and 5 deletions
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main.c
+5 -2
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.1.1-r364-dirty"
#define MM_VERSION "2.1.1-r365-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -36,6 +36,7 @@ static struct option long_options[] = {
{ "splice", no_argument, 0, 0 },
{ "cost-non-gt-ag", required_argument, 0, 0 },
{ "no-sam-sq", no_argument, 0, 0 },
{ "approx-ext", no_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -113,6 +114,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==10) opt.flag |= MM_F_SPLICE; // --splice
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_APPROX_EXT; // --approx-ext
else if (c == 'V') {
puts(MM_VERSION);
return 0;
@@ -163,7 +165,7 @@ int main(int argc, char *argv[])
} else if (strcmp(optarg, "short") == 0 || strcmp(optarg, "sr") == 0) {
k = 21, w = 11, is_hpc = 0;
minibatch_size = 50000000;
opt.flag |= MM_F_SR;
opt.flag |= MM_F_APPROX_EXT;
opt.a = 2, opt.b = 8, opt.q = 12, opt.e = 2, opt.q2 = 32, opt.e2 = 1;
opt.max_gap = 100;
opt.pri_ratio = 0.5f;
@@ -237,6 +239,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n");
fprintf(fp_help, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n");
fprintf(fp_help, " splice: long-read spliced alignment (see minimap2.1 for details)\n");
fprintf(fp_help, " sr: short single-end reads without splicing (see minimap2.1 for details)\n");
fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");
return fp_help == stdout? 0 : 1;
}