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

diff --git src/htslib/cram/cram_index.h src/htslib/cram/cram_index.h
deleted file mode 100644
index c0429e05c11..00000000000
--- src/htslib/cram/cram_index.h
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
-Copyright (c) 2013 Genome Research Ltd.
-Author: James Bonfield <jkb@sanger.ac.uk>
-
-Redistribution and use in source and binary forms, with or without 
-modification, are permitted provided that the following conditions are met:
-
-   1. Redistributions of source code must retain the above copyright notice, 
-this list of conditions and the following disclaimer.
-
-   2. Redistributions in binary form must reproduce the above copyright notice, 
-this list of conditions and the following disclaimer in the documentation 
-and/or other materials provided with the distribution.
-
-   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
-Institute nor the names of its contributors may be used to endorse or promote
-products derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
-DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-*/
-
-#ifndef _CRAM_INDEX_H_
-#define _CRAM_INDEX_H_
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/*
- * Loads a CRAM .crai index into memory.
- * Returns 0 for success
- *        -1 for failure
- */
-int cram_index_load(cram_fd *fd, const char *fn, const char *fn_idx);
-
-void cram_index_free(cram_fd *fd);
-
-/*
- * Searches the index for the first slice overlapping a reference ID
- * and position.
- *
- * Returns the cram_index pointer on sucess
- *         NULL on failure
- */
-cram_index *cram_index_query(cram_fd *fd, int refid, int pos, cram_index *frm);
-
-/*
- * Skips to a container overlapping the start coordinate listed in
- * cram_range.
- *
- * Returns 0 on success
- *        -1 on failure
- */
-int cram_seek_to_refpos(cram_fd *fd, cram_range *r);
-
-void cram_index_free(cram_fd *fd);
-
-/*
- * Skips to a container overlapping the start coordinate listed in
- * cram_range.
- *
- * In theory we call cram_index_query multiple times, once per slice
- * overlapping the range. However slices may be absent from the index
- * which makes this problematic. Instead we find the left-most slice
- * and then read from then on, skipping decoding of slices and/or
- * whole containers when they don't overlap the specified cram_range.
- *
- * Returns 0 on success
- *        -1 on failure
- */
-int cram_seek_to_refpos(cram_fd *fd, cram_range *r);
-
-/*
- * Builds an index file.
- *
- * fd is a newly opened cram file that we wish to index.
- * fn_base is the filename of the associated CRAM file.
- * fn_idx is the filename of the index file to be written;
- * if NULL, we add ".crai" to fn_base to get the index filename.
- *
- * Returns 0 on success
- *        -1 on failure
- */
-int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif