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

diff --git src/htslib/htslib/tbx.h src/htslib/htslib/tbx.h
deleted file mode 100644
index 65243b96b3b..00000000000
--- src/htslib/htslib/tbx.h
+++ /dev/null
@@ -1,79 +0,0 @@
-/*  tbx.h -- tabix API functions.
-
-    Copyright (C) 2009, 2012-2015 Genome Research Ltd.
-    Copyright (C) 2010, 2012 Broad Institute.
-
-    Author: Heng Li <lh3@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_TBX_H
-#define HTSLIB_TBX_H
-
-#include "hts.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#define TBX_MAX_SHIFT 31
-
-#define TBX_GENERIC 0
-#define TBX_SAM     1
-#define TBX_VCF     2
-#define TBX_UCSC    0x10000
-
-typedef struct {
-    int32_t preset;
-    int32_t sc, bc, ec; // seq col., beg col. and end col.
-    int32_t meta_char, line_skip;
-} tbx_conf_t;
-
-typedef struct {
-    tbx_conf_t conf;
-    hts_idx_t *idx;
-    void *dict;
-} tbx_t;
-
-extern tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sam, tbx_conf_vcf;
-
-    #define tbx_itr_destroy(iter) hts_itr_destroy(iter)
-    #define tbx_itr_queryi(tbx, tid, beg, end) hts_itr_query((tbx)->idx, (tid), (beg), (end), tbx_readrec)
-    #define tbx_itr_querys(tbx, s) hts_itr_querys((tbx)->idx, (s), (hts_name2id_f)(tbx_name2id), (tbx), hts_itr_query, tbx_readrec)
-    #define tbx_itr_next(htsfp, tbx, itr, r) hts_itr_next(hts_get_bgzfp(htsfp), (itr), (r), (tbx))
-    #define tbx_bgzf_itr_next(bgzfp, tbx, itr, r) hts_itr_next((bgzfp), (itr), (r), (tbx))
-
-    int tbx_name2id(tbx_t *tbx, const char *ss);
-
-    /* Internal helper function used by tbx_itr_next() */
-    BGZF *hts_get_bgzfp(htsFile *fp);
-    int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end);
-
-    int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf);
-    int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf);
-    tbx_t *tbx_index_load(const char *fn);
-    tbx_t *tbx_index_load2(const char *fn, const char *fnidx);
-    const char **tbx_seqnames(tbx_t *tbx, int *n);  // free the array but not the values
-    void tbx_destroy(tbx_t *tbx);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif