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Use FNV1a for string hashing #1806

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Jul 18, 2024
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Use FNV1a for string hashing #1806

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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@ shlib-exports-*.txt
/test/test_index
/test/test_introspection
/test/test_kfunc
/test/test_khash
/test/test_kstring
/test/test_mod
/test/test_nibbles
Expand Down
6 changes: 6 additions & 0 deletions Makefile
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Expand Up @@ -85,6 +85,7 @@ BUILT_TEST_PROGRAMS = \
test/test_expr \
test/test_faidx \
test/test_kfunc \
test/test_khash \
test/test_kstring \
test/test_mod \
test/test_nibbles \
Expand Down Expand Up @@ -605,6 +606,7 @@ check test: all $(HTSCODECS_TEST_TARGETS)
test/hts_endian
test/test_expr
test/test_kfunc
test/test_khash
test/test_kstring
test/test_nibbles -v
test/test_str2int
Expand Down Expand Up @@ -669,6 +671,9 @@ test/test_faidx: test/test_faidx.o libhts.a
test/test_kfunc: test/test_kfunc.o libhts.a
$(CC) $(LDFLAGS) -o $@ test/test_kfunc.o libhts.a -lz $(LIBS) -lpthread

test/test_khash: test/test_khash.o libhts.a
$(CC) $(LDFLAGS) -o $@ test/test_khash.o libhts.a -lz $(LIBS) -lpthread

test/test_kstring: test/test_kstring.o libhts.a
$(CC) $(LDFLAGS) -o $@ test/test_kstring.o libhts.a -lz $(LIBS) -lpthread

Expand Down Expand Up @@ -778,6 +783,7 @@ test/sam.o: test/sam.c config.h $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_fa
test/test_bgzf.o: test/test_bgzf.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_hts_log_h) $(hfile_internal_h)
test/test_expr.o: test/test_expr.c config.h $(htslib_hts_expr_h)
test/test_kfunc.o: test/test_kfunc.c config.h $(htslib_kfunc_h)
test/test_khash.o: test/test_khash.c config.h $(htslib_khash_h) $(htslib_kroundup_h)
test/test_kstring.o: test/test_kstring.c config.h $(htslib_kstring_h)
test/test_mod.o: test/test_mod.c config.h $(htslib_sam_h)
test/test_nibbles.o: test/test_nibbles.c config.h $(htslib_sam_h) $(sam_internal_h)
Expand Down
87 changes: 83 additions & 4 deletions htslib/khash.h
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@@ -1,7 +1,7 @@
/* The MIT License

Copyright (c) 2008, 2009, 2011 by Attractive Chaos <[email protected]>
Copyright (C) 2014-2015, 2018 Genome Research Ltd.
Copyright (C) 2014-2015, 2018, 2024 Genome Research Ltd.

Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
Expand Down Expand Up @@ -356,7 +356,39 @@ static const double __ac_HASH_UPPER = 0.77;
__ac_set_isdel_true(h->flags, x); \
--h->size; \
} \
}
} \
SCOPE int kh_stats_##name(kh_##name##_t *h, khint_t *empty, \
khint_t *deleted, khint_t *hist_size, \
khint_t **hist_out) \
{ \
khint_t i, *hist = NULL, dist_max = 0, k, dist, step; \
khint_t mask = h->n_buckets - 1; \
*empty = *deleted = *hist_size = 0; \
hist = (khint_t *) calloc(1, sizeof(*hist)); \
if (!hist) { return -1; } \
for (i = kh_begin(h); i < kh_end(h); ++i) { \
if (__ac_isempty(h->flags, i)) { (*empty)++; continue; } \
if (__ac_isdel(h->flags, i)) { (*deleted)++; continue; } \
k = __hash_func(h->keys[i]) & (h->n_buckets - 1); \
dist = 0; \
step = 0; \
while (k != i) { \
dist++; \
k = (k + (++step)) & mask; \
} \
if (dist_max <= dist) { \
khint_t *new_hist = (khint_t *) realloc(hist, sizeof(*new_hist) * (dist + 1)); \
if (!new_hist) { free(hist); return -1; } \
for (k = dist_max + 1; k <= dist; k++) new_hist[k] = 0; \
hist = new_hist; \
dist_max = dist; \
} \
hist[dist]++; \
} \
*hist_out = hist; \
*hist_size = dist_max + 1; \
return 0; \
}

#define KHASH_DECLARE(name, khkey_t, khval_t) \
__KHASH_TYPE(name, khkey_t, khval_t) \
Expand Down Expand Up @@ -391,6 +423,7 @@ static const double __ac_HASH_UPPER = 0.77;
@abstract 64-bit integer comparison function
*/
#define kh_int64_hash_equal(a, b) ((a) == (b))

/*! @function
@abstract const char* hash function
@param s Pointer to a null terminated string
Expand All @@ -402,12 +435,28 @@ static kh_inline khint_t __ac_X31_hash_string(const char *s)
if (h) for (++s ; *s; ++s) h = (h << 5) - h + (khint_t)*s;
return h;
}

/*! @function
@abstract const char* FNV1a hash function
@param s Pointer to a null terminated string
@return The hash value
*/
static kh_inline khint_t __ac_FNV1a_hash_string(const char *s)
{
const khint_t offset_basis = 2166136261;
const khint_t FNV_prime = 16777619;
khint_t h = offset_basis;
for (; *s; ++s) h = (h ^ (uint8_t) *s) * FNV_prime;
return h;
}

/*! @function
@abstract Another interface to const char* hash function
@param key Pointer to a nul terminated string [const char*]
@return The hash value [khint_t]
*/
#define kh_str_hash_func(key) __ac_X31_hash_string(key)
#define kh_str_hash_func(key) __ac_FNV1a_hash_string(key)

/*! @function
@abstract Const char* comparison function
*/
Expand All @@ -426,12 +475,29 @@ static kh_inline khint_t __ac_X31_hash_kstring(const kstring_t ks)
h = (h << 5) - h + (khint_t)ks.s[i];
return h;
}

/*! @function
@abstract Kstring hash function
@param s Pointer to a kstring
@return The hash value
*/
static kh_inline khint_t __ac_FNV1a_hash_kstring(const kstring_t ks)
{
const khint_t offset_basis = 2166136261;
const khint_t FNV_prime = 16777619;
khint_t h = offset_basis;
size_t i;
for (i = 0; i < ks.l; i++)
h = (h ^ (uint8_t) ks.s[i]) * FNV_prime;
return h;
}

/*! @function
@abstract Interface to kstring hash function.
@param key Pointer to a khash; permits hashing on non-nul terminated strings.
@return The hash value [khint_t]
*/
#define kh_kstr_hash_func(key) __ac_X31_hash_kstring(key)
#define kh_kstr_hash_func(key) __ac_FNV1a_hash_kstring(key)
/*! @function
@abstract kstring comparison function
*/
Expand Down Expand Up @@ -604,6 +670,19 @@ static kh_inline khint_t __ac_Wang_hash(khint_t key)
code; \
} }

/*! @function
@abstract Gather hash table statistics
@param name Name of the hash table [symbol]
@param h Pointer to the hash table [khash_t(name)*]
@param empty[out] Number of empty hash bins
@param deleted[out] Number of hash bins with the deleted flag
@param hist_size[out] Size of @p hist array
@param hist[out] Probe count histogram
@return 0 on success; -1 on failure
*/
#define kh_stats(name, h, empty, deleted, hist_size, hist) \
kh_stats_##name(h, empty, deleted, hist_size, hist)

/* More convenient interfaces */

/*! @function
Expand Down
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