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

diff --git src/htslib/htslib/faidx.h src/htslib/htslib/faidx.h
deleted file mode 100644
index f44bf00021f..00000000000
--- src/htslib/htslib/faidx.h
+++ /dev/null
@@ -1,137 +0,0 @@
-/* faidx.h -- FASTA random access.
-
-   Copyright (C) 2008, 2009, 2013, 2014 Genome Research Ltd.
-
-   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_FAIDX_H
-#define HTSLIB_FAIDX_H
-
-#include "hts_defs.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/*!
-  @header
-
-  Index FASTA files and extract subsequence.
-
-  The fai file index columns are:
-    - chromosome name
-    - chromosome length: number of bases
-    - offset: number of bytes to skip to get to the first base
-        from the beginning of the file, including the length
-        of the sequence description string (">chr ..\n")
-    - line length: number of bases per line (excluding \n)
-    - binary line length: number of bytes, including \n
-
-  @copyright The Wellcome Trust Sanger Institute.
- */
-
-struct __faidx_t;
-typedef struct __faidx_t faidx_t;
-
-    /*!
-      @abstract   Build index for a FASTA or bgzip-compressed FASTA file.
-      @param  fn  FASTA file name
-      @return     0 on success; or -1 on failure
-      @discussion File "fn.fai" will be generated.
-     */
-    int fai_build(const char *fn);
-
-    /*!
-      @abstract    Destroy a faidx_t struct.
-      @param  fai  Pointer to the struct to be destroyed
-     */
-    void fai_destroy(faidx_t *fai);
-
-    /*!
-      @abstract   Load index from "fn.fai".
-      @param  fn  File name of the FASTA file
-     */
-    faidx_t *fai_load(const char *fn);
-
-    /*!
-      @abstract    Fetch the sequence in a region.
-      @param  fai  Pointer to the faidx_t struct
-      @param  reg  Region in the format "chr2:20,000-30,000"
-      @param  len  Length of the region; -2 if seq not present, -1 general error
-      @return      Pointer to the sequence; null on failure
-
-      @discussion The returned sequence is allocated by malloc family
-      and should be destroyed by end users by calling free() on it.
-     */
-    char *fai_fetch(const faidx_t *fai, const char *reg, int *len);
-
-    /*!
-      @abstract    Fetch the number of sequences.
-      @param  fai  Pointer to the faidx_t struct
-      @return      The number of sequences
-     */
-    int faidx_fetch_nseq(const faidx_t *fai) HTS_DEPRECATED("Please use faidx_nseq instead");
-
-    /*!
-      @abstract    Fetch the sequence in a region.
-      @param  fai  Pointer to the faidx_t struct
-      @param  c_name Region name
-      @param  p_beg_i  Beginning position number (zero-based)
-      @param  p_end_i  End position number (zero-based)
-      @param  len  Length of the region; -2 if c_name not present, -1 general error
-      @return      Pointer to the sequence; null on failure
-
-      @discussion The returned sequence is allocated by malloc family
-      and should be destroyed by end users by calling free() on it.
-     */
-    char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
-
-    /*!
-      @abstract    Query if sequence is present
-      @param  fai  Pointer to the faidx_t struct
-      @param  seq  Sequence name
-      @return      1 if present or 0 if absent
-     */
-    int faidx_has_seq(const faidx_t *fai, const char *seq);
-
-    /*!
-      @abstract    Return number of sequences in fai index
-     */
-    int faidx_nseq(const faidx_t *fai);
-
-    /*!
-      @abstract    Return name of i-th sequence
-     */
-    const char *faidx_iseq(const faidx_t *fai, int i);
-
-    /*!
-      @abstract    Return sequence length, -1 if not present
-     */
-    int faidx_seq_len(const faidx_t *fai, const char *seq);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif