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Speed up faidx. #1797

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Jul 8, 2024
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Speed up faidx. #1797

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26 changes: 25 additions & 1 deletion faidx.c
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,29 @@ DEALINGS IN THE SOFTWARE. */
#include "htslib/kstring.h"
#include "hts_internal.h"

// Faster isgraph; assumes ASCII
static inline int isgraph_(unsigned char c) {
return c > ' ' && c <= '~';
}

#ifdef isgraph
# undef isgraph
#endif
#define isgraph isgraph_

// An optimised bgzf_getc.
// We could consider moving this to bgzf.h, but our own code uses it here only.
static inline int bgzf_getc_(BGZF *fp) {
if (fp->block_offset+1 < fp->block_length) {
int c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
fp->uncompressed_address++;
return c;
}

return bgzf_getc(fp);
}
#define bgzf_getc bgzf_getc_

typedef struct {
int id; // faidx_t->name[id] is for this struct.
uint32_t line_len, line_blen;
Expand Down Expand Up @@ -727,7 +750,8 @@ static char *fai_retrieve(const faidx_t *fai, const faidx1_t *val,
return NULL;
}

while ( l < end - beg && (c=bgzf_getc(fai->bgzf))>=0 )
BGZF *fp = fai->bgzf;
while ( l < end - beg && (c=bgzf_getc(fp))>=0 )
if (isgraph(c)) s[l++] = c;
if (c < 0) {
hts_log_error("Failed to retrieve block: %s",
Expand Down