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[cover] Optimize case where d <= 8

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This commit is contained in:
Nick Terrell
2017-05-02 11:02:43 -07:00
parent 865918dd04
commit f2d9ef1dc0
3 changed files with 34 additions and 10 deletions
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lib/dictBuilder/cover.c
+30 -7
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@@ -234,10 +234,22 @@ static size_t COVER_sum(const size_t *samplesSizes, unsigned nbSamples) {
* Returns 1 if the dmer at lp is greater than the dmer at rp.
*/
static int COVER_cmp(COVER_ctx_t *ctx, const void *lp, const void *rp) {
const U32 lhs = *(const U32 *)lp;
const U32 rhs = *(const U32 *)rp;
U32 const lhs = *(U32 const *)lp;
U32 const rhs = *(U32 const *)rp;
return memcmp(ctx->samples + lhs, ctx->samples + rhs, ctx->d);
}
/**
* Faster version for d <= 8.
*/
static int COVER_cmp8(COVER_ctx_t *ctx, const void *lp, const void *rp) {
U64 const mask = (ctx->d == 8) ? (U64)-1 : (((U64)1 << (8 * ctx->d)) - 1);
U64 const lhs = MEM_readLE64(ctx->samples + *(U32 const *)lp) & mask;
U64 const rhs = MEM_readLE64(ctx->samples + *(U32 const *)rp) & mask;
if (lhs < rhs) {
return -1;
}
return (lhs > rhs);
}
/**
* Same as COVER_cmp() except ties are broken by pointer value
@@ -251,6 +263,16 @@ static int COVER_strict_cmp(const void *lp, const void *rp) {
}
return result;
}
/**
* Faster version for d <= 8.
*/
static int COVER_strict_cmp8(const void *lp, const void *rp) {
int result = COVER_cmp8(g_ctx, lp, rp);
if (result == 0) {
result = lp < rp ? -1 : 1;
}
return result;
}
/**
* Returns the first pointer in [first, last) whose element does not compare
@@ -506,7 +528,7 @@ static int COVER_ctx_init(COVER_ctx_t *ctx, const void *samplesBuffer,
const BYTE *const samples = (const BYTE *)samplesBuffer;
const size_t totalSamplesSize = COVER_sum(samplesSizes, nbSamples);
/* Checks */
if (totalSamplesSize < d ||
if (totalSamplesSize < MAX(d, sizeof(U64)) ||
totalSamplesSize >= (size_t)COVER_MAX_SAMPLES_SIZE) {
DISPLAYLEVEL(1, "Total samples size is too large, maximum size is %u MB\n",
(COVER_MAX_SAMPLES_SIZE >> 20));
@@ -520,7 +542,7 @@ static int COVER_ctx_init(COVER_ctx_t *ctx, const void *samplesBuffer,
ctx->samplesSizes = samplesSizes;
ctx->nbSamples = nbSamples;
/* Partial suffix array */
ctx->suffixSize = totalSamplesSize - d + 1;
ctx->suffixSize = totalSamplesSize - MAX(d, sizeof(U64)) + 1;
ctx->suffix = (U32 *)malloc(ctx->suffixSize * sizeof(U32));
/* Maps index to the dmerID */
ctx->dmerAt = (U32 *)malloc(ctx->suffixSize * sizeof(U32));
@@ -554,7 +576,8 @@ static int COVER_ctx_init(COVER_ctx_t *ctx, const void *samplesBuffer,
}
/* qsort doesn't take an opaque pointer, so pass as a global */
g_ctx = ctx;
qsort(ctx->suffix, ctx->suffixSize, sizeof(U32), &COVER_strict_cmp);
qsort(ctx->suffix, ctx->suffixSize, sizeof(U32),
(ctx->d <= 8 ? &COVER_strict_cmp8 : &COVER_strict_cmp));
}
DISPLAYLEVEL(2, "Computing frequencies\n");
/* For each dmer group (group of positions with the same first d bytes):
@@ -564,8 +587,8 @@ static int COVER_ctx_init(COVER_ctx_t *ctx, const void *samplesBuffer,
* 2. We calculate how many samples the dmer occurs in and save it in
* freqs[dmerId].
*/
COVER_groupBy(ctx->suffix, ctx->suffixSize, sizeof(U32), ctx, &COVER_cmp,
&COVER_group);
COVER_groupBy(ctx->suffix, ctx->suffixSize, sizeof(U32), ctx,
(ctx->d <= 8 ? &COVER_cmp8 : &COVER_cmp), &COVER_group);
ctx->freqs = ctx->suffix;
ctx->suffix = NULL;
return 1;