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dp chaining mostly works, but fails sometimes

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which means there are bugs that need to be fixed
This commit is contained in:
Heng Li
2017-06-06 14:19:50 -04:00
parent 1a9fc04cf0
commit 6d4348db44
6 changed files with 60 additions and 25 deletions
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main.c
+27 -4
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@@ -4,6 +4,7 @@
#include <string.h>
#include <sys/resource.h>
#include <sys/time.h>
#include <fcntl.h>
#include "bseq.h"
#include "minimap.h"
#include "mmpriv.h"
@@ -20,10 +21,29 @@ void liftrlimit()
#endif
}
static int test_idx(const char *fn)
{
int fd, is_idx = 0;
off_t ret;
char magic[4];
if (strcmp(fn, "-") == 0) return 0; // read from pipe; not an index
fd = open(fn, O_RDONLY);
if (fd < 0) return -1; // error
if ((ret = lseek(fd, 0, SEEK_END)) >= 4) {
lseek(fd, 0, SEEK_SET);
read(fd, magic, 4);
if (strncmp(magic, MM_IDX_MAGIC, 4) == 0)
is_idx = 1;
}
close(fd);
return is_idx;
}
int main(int argc, char *argv[])
{
mm_mapopt_t opt;
int i, c, k = 17, w = -1, b = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx = 0, is_hpc = 0;
int i, c, k = 17, w = -1, b = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0;
int mini_batch_size = 100000000;
uint64_t batch_size = 4000000000ULL;
bseq_file_t *fp = 0;
@@ -34,12 +54,11 @@ 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:NOg:I:d:lST:s:Dx:H")) >= 0) {
while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:NOg:I:d:ST:s:Dx:H")) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'b') b = atoi(optarg);
else if (c == 'H') is_hpc = 1;
else if (c == 'l') is_idx = 1;
else if (c == 'd') fnw = optarg; // the above are indexing related options, except -I
else if (c == 'r') opt.bw = atoi(optarg);
else if (c == 'f') opt.mid_occ_frac = atof(optarg);
@@ -83,7 +102,6 @@ int main(int argc, char *argv[])
fprintf(stderr, " -w INT minizer window size [{-k}*2/3]\n");
fprintf(stderr, " -I NUM split index for every ~NUM input bases [4G]\n");
fprintf(stderr, " -d FILE dump index to FILE []\n");
fprintf(stderr, " -l the 1st argument is a index file (overriding -k, -w and -I)\n");
// fprintf(stderr, " -b INT bucket bits [%d]\n", b); // most users wouldn't care about this
fprintf(stderr, " Mapping:\n");
fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%.3f]\n", opt.mid_occ_frac);
@@ -106,6 +124,11 @@ int main(int argc, char *argv[])
return 1;
}
is_idx = test_idx(argv[optind]);
if (is_idx < 0) {
fprintf(stderr, "[E::%s] failed to open file '%s'\n", __func__, argv[optind]);
return 1;
}
if (is_idx) fpr = fopen(argv[optind], "rb");
else fp = bseq_open(argv[optind]);
if (fnw) fpw = fopen(fnw, "wb");