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r188: renamed bseq* to mm_bseq*

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to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
This commit is contained in:
Heng Li
2017-07-19 09:26:46 -04:00
parent b9b0b6f49c
commit 71c988f6ab
10 changed files with 65 additions and 57 deletions
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main.c
+5 -5
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@@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r187-dirty"
#define MM_VERSION "2.0-r188-dirty"
void liftrlimit()
{
@@ -66,7 +66,7 @@ int main(int argc, char *argv[])
int i, c, k = 17, w = -1, bucket_bits = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0, long_idx;
int minibatch_size = 200000000;
uint64_t batch_size = 4000000000ULL;
bseq_file_t *fp = 0;
mm_bseq_file_t *fp = 0;
char *fnw = 0, *s;
FILE *fpr = 0, *fpw = 0;
@@ -203,12 +203,12 @@ int main(int argc, char *argv[])
return 1;
}
if (is_idx) fpr = fopen(argv[optind], "rb");
else fp = bseq_open(argv[optind]);
else fp = mm_bseq_open(argv[optind]);
if (fnw) fpw = fopen(fnw, "wb");
for (;;) {
mm_idx_t *mi = 0;
if (fpr) mi = mm_idx_load(fpr);
else if (!bseq_eof(fp))
else if (!mm_bseq_eof(fp))
mi = mm_idx_gen(fp, w, k, bucket_bits, is_hpc, minibatch_size, n_threads, batch_size, keep_name);
if (mi == 0) break;
if (mm_verbose >= 3)
@@ -227,7 +227,7 @@ int main(int argc, char *argv[])
}
if (fpw) fclose(fpw);
if (fpr) fclose(fpr);
if (fp) bseq_close(fp);
if (fp) mm_bseq_close(fp);
fprintf(stderr, "[M::%s] Version: %s\n", __func__, MM_VERSION);
fprintf(stderr, "[M::%s] CMD:", __func__);