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r829: replaced musl's getopt with ketopt

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Heng Li
2018-09-01 21:18:02 -04:00
parent 3a119d606f
commit 7998fe9906
6 changed files with 272 additions and 420 deletions
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sdust.c
+7 -6
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@@ -177,7 +177,7 @@ uint64_t *sdust(void *km, const uint8_t *seq, int l_seq, int T, int W, int *n)
#ifdef _SDUST_MAIN
#include <zlib.h>
#include <stdio.h>
#include "getopt.h"
#include "ketopt.h"
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
@@ -186,16 +186,17 @@ int main(int argc, char *argv[])
gzFile fp;
kseq_t *ks;
int W = 64, T = 20, c;
ketopt_t o = KETOPT_INIT;
while ((c = getopt(argc, argv, "w:t:")) >= 0) {
if (c == 'w') W = atoi(optarg);
else if (c == 't') T = atoi(optarg);
while ((c = ketopt(&o, argc, argv, 1, "w:t:", 0)) >= 0) {
if (c == 'w') W = atoi(o.arg);
else if (c == 't') T = atoi(o.arg);
}
if (optind == argc) {
if (o.ind == argc) {
fprintf(stderr, "Usage: sdust [-w %d] [-t %d] <in.fa>\n", W, T);
return 1;
}
fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
fp = strcmp(argv[o.ind], "-")? gzopen(argv[o.ind], "r") : gzdopen(fileno(stdin), "r");
ks = kseq_init(fp);
while (kseq_read(ks) >= 0) {
uint64_t *r;