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added prefetch and minor updates to speedup pileup #1986

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added prefetch and minor updates to speedup pileup #1986

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2fc73ac
added prefetch and minor updates to speedup pileup
vasudeva8 Feb 5, 2026
572ecc7
Add autoconf check for __builtin_prefetch
jkbonfield Feb 16, 2026
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29 changes: 29 additions & 0 deletions configure.ac
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Original file line number Diff line number Diff line change
Expand Up @@ -162,6 +162,35 @@ HTS_CHECK_COMPILE_FLAGS_NEEDED([avx512f], [-mavx512f -mpopcnt],
AC_DEFINE([HAVE_AVX512],1,[Defined to 1 if rANS source using AVX512F can be compiled.])
])

dnl Check for presence of builtin_clz
AC_MSG_CHECKING([for working __builtin_clz])
AC_LINK_IFELSE([AC_LANG_PROGRAM([],[
int z = 10;
if (__builtin_clz(z)) {
return 0;
}
])], [
AC_MSG_RESULT([yes])
AC_DEFINE([HAVE___BUILTIN_CLZ], 1,
[Defined to 1 if __builtin_clz works])
], [
AC_MSG_RESULT([no])
])

dnl Check for presence of builtin_prefetch
AC_MSG_CHECKING([for working __builtin_prefetch])
AC_LINK_IFELSE([AC_LANG_PROGRAM([],[
int z = 10;
__builtin_prefetch(&z);
return 0;
])], [
AC_MSG_RESULT([yes])
AC_DEFINE([HAVE___BUILTIN_PREFETCH], 1,
[Defined to 1 if __builtin_prefetch works])
], [
AC_MSG_RESULT([no])
])

dnl Check for working __builtin_cpu_supports (ssse3 is broken on some clangs)
AC_MSG_CHECKING([for working __builtin_cpu_supports("ssse3")])
AC_LINK_IFELSE([AC_LANG_PROGRAM([],[
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13 changes: 13 additions & 0 deletions htslib/hts_defs.h
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Expand Up @@ -138,4 +138,17 @@ DEALINGS IN THE SOFTWARE. */
#define HTSLIB_EXPORT
#endif

// Prefetch implementations.
// We only support a basic implementation here
#ifdef HAVE___BUILTIN_PREFETCH
static inline void hts_prefetch(void *p) {
__builtin_prefetch(p);
}
#else
static inline void hts_prefetch(void *p) {
// Fetch and discard is quite close to a genuine prefetch
*(volatile char *)p;
}
#endif

#endif
5 changes: 5 additions & 0 deletions sam.c
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Expand Up @@ -5977,6 +5977,9 @@ static void overlap_remove(bam_plp_t iter, const bam1_t *b)
{
if ( !iter->overlaps ) return;

if ( b->core.flag&BAM_FUNMAP || !(b->core.flag&BAM_FPROPER_PAIR) ) //no need
return;

khiter_t kitr;
if ( b )
{
Expand Down Expand Up @@ -6007,6 +6010,8 @@ const bam_pileup1_t *bam_plp64_next(bam_plp_t iter, int *_tid, hts_pos_t *_pos,
// write iter->plp at iter->pos
lbnode_t **pptr = &iter->head;
while (*pptr != iter->tail) {
if ((*pptr)->next)
hts_prefetch((*pptr)->next);
lbnode_t *p = *pptr;
if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove
overlap_remove(iter, &p->b);
Expand Down