7df6e18265341f87a69fba808aa1f92f8ebca841
markd
  Wed Apr 15 13:39:42 2026 -0700
move copy of htslib

diff --git src/htslib/htslib/khash_str2int.h src/htslib/htslib/khash_str2int.h
deleted file mode 100644
index 4bbc10088f7..00000000000
--- src/htslib/htslib/khash_str2int.h
+++ /dev/null
@@ -1,133 +0,0 @@
-/*  khash_str2int.h -- C-string to integer hash table.
-
-    Copyright (C) 2013 Genome Research Ltd.
-
-    Author: Petr Danecek <pd3@sanger.ac.uk>
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-DEALINGS IN THE SOFTWARE.  */
-
-#ifndef HTSLIB_KHASH_STR2INT_H
-#define HTSLIB_KHASH_STR2INT_H
-
-#include <htslib/khash.h>
-
-KHASH_MAP_INIT_STR(str2int, int)
-
-/*
- *  Wrappers for khash dictionaries used by mpileup.
- */
-
-static inline void *khash_str2int_init(void)
-{
-    return kh_init(str2int);
-}
-
-/*
- *  Destroy the hash structure, but not the keys
- */
-static inline void khash_str2int_destroy(void *_hash)
-{
-    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
-    if (hash) kh_destroy(str2int, hash); // Note that strings are not freed.
-}
-
-/*
- *  Destroys both the hash structure and the keys
- */
-static inline void khash_str2int_destroy_free(void *_hash)
-{
-    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
-    khint_t k;
-    if (hash == 0) return;
-    for (k = 0; k < kh_end(hash); ++k)
-        if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
-    kh_destroy(str2int, hash);
-}
-
-/*
- *  Returns 1 if key exists or 0 if not
- */
-static inline int khash_str2int_has_key(void *_hash, const char *str)
-{
-    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
-    khint_t k = kh_get(str2int, hash, str);
-    if ( k == kh_end(hash) ) return 0;
-    return 1;
-}
-
-/*
- *  Returns 0 on success and -1 when the key is not present. On success,
- *  *value is set, unless NULL is passed.
- */
-static inline int khash_str2int_get(void *_hash, const char *str, int *value)
-{
-    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
-    khint_t k;
-    if ( !hash ) return -1;
-    k = kh_get(str2int, hash, str);
-    if ( k == kh_end(hash) ) return -1;
-    if ( !value ) return 0;
-    *value = kh_val(hash, k);
-    return 0;
-}
-
-/*
- *  Add a new string to the dictionary, auto-incrementing the value.
- *  On success returns the newly inserted integer id, on error -1
- *  is returned. Note that the key must continue to exist throughout
- *  the whole life of _hash.
- */
-static inline int khash_str2int_inc(void *_hash, const char *str)
-{
-    khint_t k;
-    int ret;
-    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
-    if ( !hash ) return -1;
-    k = kh_put(str2int, hash, str, &ret);
-    if (ret == 0) return kh_val(hash, k);
-    kh_val(hash, k) = kh_size(hash) - 1;
-    return kh_val(hash, k);
-}
-
-/*
- *  Set a new key,value pair. On success returns the bin index, on
- *  error -1 is returned. Note that the key must contnue to exist
- *  throughout the whole life of _hash.
- */
-static inline int khash_str2int_set(void *_hash, const char *str, int value)
-{
-    khint_t k;
-    int ret;
-    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
-    if ( !hash ) return -1;
-    k = kh_put(str2int, hash, str, &ret);
-    kh_val(hash,k) = value;
-    return k;
-}
-
-/*
- *  Return the number of keys in the hash table.
- */
-static inline int khash_str2int_size(void *_hash)
-{
-    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
-    return kh_size(hash);
-}
-
-#endif