zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

r625: HPC sketch still has one minor issue

This commit is contained in:
Heng Li 2017-12-13 09:40:42 -05:00
parent ae85dcde76
commit d003a00d71
2 changed files with 9 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.6-r623"
#define MM_VERSION "2.6-r625-dirty"
#ifdef __linux__
#include <sys/resource.h>

16
sketch.c
View File

@ -113,26 +113,26 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
}
} else l = 0, tq.count = tq.front = 0, kmer_span = 0;
buf[buf_pos] = info; // need to do this here as appropriate buf_pos and buf[buf_pos] are needed below
if (l == w + k - 1) { // special case for the first window - because identical k-mers are not stored yet
if (l == w + k - 1 && min.x != UINT64_MAX) { // special case for the first window - because identical k-mers are not stored yet
for (j = buf_pos + 1; j < w; ++j)
if (min.x == buf[j].x && buf[j].y != min.y && buf[j].y != UINT64_MAX) kv_push(mm128_t, km, *p, buf[j]);
if (min.x == buf[j].x && buf[j].y != min.y) kv_push(mm128_t, km, *p, buf[j]);
for (j = 0; j < buf_pos; ++j)
if (min.x == buf[j].x && buf[j].y != min.y && buf[j].y != UINT64_MAX) kv_push(mm128_t, km, *p, buf[j]);
if (min.x == buf[j].x && buf[j].y != min.y) kv_push(mm128_t, km, *p, buf[j]);
}
if (info.x <= min.x) { // a new minimum; then write the old min
if (l >= w + k && min.y != UINT64_MAX) kv_push(mm128_t, km, *p, min);
if (l >= w + k && min.x != UINT64_MAX) kv_push(mm128_t, km, *p, min);
min = info, min_pos = buf_pos;
} else if (buf_pos == min_pos) { // old min has moved outside the window
if (l >= w + k - 1) kv_push(mm128_t, km, *p, min);
if (l >= w + k - 1 && min.x != UINT64_MAX) kv_push(mm128_t, km, *p, min);
for (j = buf_pos + 1, min.x = UINT64_MAX; j < w; ++j) // the two loops are necessary when there are identical k-mers
if (min.x >= buf[j].x) min = buf[j], min_pos = j; // >= is important s.t. min is always the closest k-mer
for (j = 0; j <= buf_pos; ++j)
if (min.x >= buf[j].x) min = buf[j], min_pos = j;
if (l >= w + k - 1) { // write identical k-mers
if (l >= w + k - 1 && min.x != UINT64_MAX) { // write identical k-mers
for (j = buf_pos + 1; j < w; ++j) // these two loops make sure the output is sorted
if (min.x == buf[j].x && min.y != buf[j].y && buf[j].y != UINT64_MAX) kv_push(mm128_t, km, *p, buf[j]);
if (min.x == buf[j].x && min.y != buf[j].y) kv_push(mm128_t, km, *p, buf[j]);
for (j = 0; j <= buf_pos; ++j)
if (min.x == buf[j].x && min.y != buf[j].y && buf[j].y != UINT64_MAX) kv_push(mm128_t, km, *p, buf[j]);
if (min.x == buf[j].x && min.y != buf[j].y) kv_push(mm128_t, km, *p, buf[j]);
}
}
if (++buf_pos == w) buf_pos = 0;