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

diff --git src/htslib/cram/cram_encode.h src/htslib/cram/cram_encode.h
deleted file mode 100644
index 9131d6ea902..00000000000
--- src/htslib/cram/cram_encode.h
+++ /dev/null
@@ -1,105 +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 encoding portion of CRAM I/O. Also see
- * cram_codecs.[ch] for the actual encoding functions themselves.
- */
-
-#ifndef _CRAM_WRITE_H_
-#define _CRAM_WRITE_H_
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/* ----------------------------------------------------------------------
- * CRAM sequence iterators.
- */
-
-/*! Write iterator: put BAM format sequences into a CRAM file.
- *
- * We buffer up a containers worth of data at a time.
- *
- * FIXME: break this into smaller pieces.
- *
- * @return
- * Returns 0 on success;
- *        -1 on failure
- */
-int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b);
-
-
-/* ----------------------------------------------------------------------
- * Internal functions
- */
-
-/*! INTERNAL:
- * Encodes a compression header block into a generic cram_block structure.
- *
- * @return
- * Returns cram_block ptr on success;
- *         NULL on failure
- */
-cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c,
-					   cram_block_compression_hdr *h);
-
-/*! INTERNAL:
- * Encodes a slice compression header. 
- *
- * @return
- * Returns cram_block on success;
- *         NULL on failure
- */
-cram_block *cram_encode_slice_header(cram_fd *fd, cram_slice *s);
-
-/*! INTERNAL:
- * Encodes all slices in a container into blocks.
- *
- * @return
- * Returns 0 on success;
- *        -1 on failure
- *
- * FIXME: separate into encode_container and write_container. Ideally
- * we should be able to do read_container / write_container or
- * decode_container / encode_container.
- */
-int cram_encode_container(cram_fd *fd, cram_container *c);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif