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

diff --git src/htslib/cram/cram_decode.h src/htslib/cram/cram_decode.h
deleted file mode 100644
index 64b188e25c2..00000000000
--- src/htslib/cram/cram_decode.h
+++ /dev/null
@@ -1,112 +0,0 @@
-/*
-Copyright (c) 2012-2013 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.
-*/
-
-/*! \file
- * Include cram.h instead.
- *
- * This is an internal part of the CRAM system and is automatically included
- * when you #include cram.h.
- *
- * Implements the decoding portion of CRAM I/O. Also see
- * cram_codecs.[ch] for the actual encoding functions themselves.
- */
-
-#ifndef _CRAM_READ_H_
-#define _CRAM_READ_H_
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/* ----------------------------------------------------------------------
- * CRAM sequence iterators.
- */
-
-/*! Read the next cram record and return it as a cram_record.
- *
- * Note that to decode cram_record the caller will need to look up some data
- * in the current slice, pointed to by fd->ctr->slice. This is valid until
- * the next call to cram_get_seq (which may invalidate it).
- *
- * @return
- * Returns record pointer on success (do not free);
- *        NULL on failure
- */
-cram_record *cram_get_seq(cram_fd *fd);
-
-/*! Read the next cram record and convert it to a bam_seq_t struct.
- *
- * @return
- * Returns 0 on success;
- *        -1 on EOF or failure (check fd->err)
- */
-int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam);
-
-
-/* ----------------------------------------------------------------------
- * Internal functions
- */
-
-/*! INTERNAL:
- * Decodes a CRAM block compression header.
- *
- * @return
- * Returns header ptr on success;
- *         NULL on failure
- */
-cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd,
-							   cram_block *b);
-
-/*! INTERNAL:
- * Decodes a CRAM (un)mapped slice header block.
- *
- * @return
- * Returns slice header ptr on success;
- *         NULL on failure
- */
-cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b);
-
-
-/*! INTERNAL:
- * Decode an entire slice from container blocks. Fills out s->crecs[] array.
- *
- * @return
- * Returns 0 on success;
- *        -1 on failure
- */
-int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
-		      SAM_hdr *hdr);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif