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sam output

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This commit is contained in:
Heng Li
2017-06-25 22:05:20 -04:00
parent 39083be9ab
commit b1077ff14c
5 changed files with 71 additions and 8 deletions
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main.c
+8 -1
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@@ -54,7 +54,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hp:m:z:")) >= 0) {
while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hp:m:z:F:")) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'b') b = atoi(optarg);
@@ -85,6 +85,13 @@ int main(int argc, char *argv[])
else if (*p == 'K' || *p == 'k') x *= 1e3;
if (c == 'B') mini_batch_size = (uint64_t)(x + .499);
else batch_size = (uint64_t)(x + .499);
} else if (c == 'F') {
if (strcmp(optarg, "sam") == 0) opt.flag |= MM_F_OUT_SAM;
else if (strcmp(optarg, "paf") == 0) opt.flag &= ~MM_F_OUT_SAM;
else {
fprintf(stderr, "[E::%s] unknown output format '%s'\n", __func__, optarg);
return 0;
}
} else if (c == 'x') {
if (strcmp(optarg, "ava10k") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF;