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r606: fixed a sketch bug for long 256bp k-mer

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sketch() writes {-1,-1} to the output array.
This commit is contained in:
Heng Li
2017-12-06 16:13:29 -05:00
parent 76206f574f
commit 68c63f2d68
3 changed files with 63 additions and 6 deletions
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sketch.c
+5 -5
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@@ -115,12 +115,12 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
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
for (j = buf_pos + 1; j < w; ++j)
if (min.x == buf[j].x && buf[j].y != min.y) kv_push(mm128_t, km, *p, buf[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]);
for (j = 0; j < buf_pos; ++j)
if (min.x == buf[j].x && buf[j].y != min.y) kv_push(mm128_t, km, *p, buf[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 (info.x <= min.x) { // a new minimum; then write the old min
if (l >= w + k) kv_push(mm128_t, km, *p, min);
if (l >= w + k && min.y != 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);
@@ -130,9 +130,9 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
if (min.x >= buf[j].x) min = buf[j], min_pos = j;
if (l >= w + k - 1) { // 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) kv_push(mm128_t, km, *p, buf[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]);
for (j = 0; j <= buf_pos; ++j)
if (min.x == buf[j].x && min.y != buf[j].y) kv_push(mm128_t, km, *p, buf[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 (++buf_pos == w) buf_pos = 0;