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

diff --git src/htslib/cram/cram_samtools.h src/htslib/cram/cram_samtools.h
deleted file mode 100644
index 635e2e029c1..00000000000
--- src/htslib/cram/cram_samtools.h
+++ /dev/null
@@ -1,105 +0,0 @@
-/*
-Copyright (c) 2010-2013 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_SAMTOOLS_H_
-#define _CRAM_SAMTOOLS_H_
-
-/* Samtools compatible API */
-#define bam_blk_size(b)  ((b)->l_data)
-#define bam_set_blk_size(b,v) ((b)->data_len = (v))
-
-#define bam_ref(b)       (b)->core.tid
-#define bam_pos(b)       (b)->core.pos
-#define bam_mate_pos(b)  (b)->core.mpos
-#define bam_mate_ref(b)  (b)->core.mtid
-#define bam_ins_size(b)  (b)->core.isize
-#define bam_seq_len(b)   (b)->core.l_qseq
-#define bam_cigar_len(b) (b)->core.n_cigar
-#define bam_flag(b)      (b)->core.flag
-#define bam_bin(b)       (b)->core.bin
-#define bam_map_qual(b)  (b)->core.qual
-#define bam_name_len(b)  (b)->core.l_qname
-#define bam_name(b)      bam_get_qname((b))
-#define bam_qual(b)      bam_get_qual((b))
-#define bam_seq(b)       bam_get_seq((b))
-#define bam_cigar(b)     bam_get_cigar((b))
-#define bam_aux(b)       bam_get_aux((b))
-
-#define bam_dup(b)       bam_copy1(bam_init1(), (b))
-
-#define bam_free(b)      bam_destroy1((b))
-
-#define bam_reg2bin(beg,end) hts_reg2bin((beg),(end),14,5)
-
-#include "htslib/sam.h"
-
-enum cigar_op {
-    BAM_CMATCH_=BAM_CMATCH,
-    BAM_CINS_=BAM_CINS,
-    BAM_CDEL_=BAM_CDEL,
-    BAM_CREF_SKIP_=BAM_CREF_SKIP,
-    BAM_CSOFT_CLIP_=BAM_CSOFT_CLIP,
-    BAM_CHARD_CLIP_=BAM_CHARD_CLIP,
-    BAM_CPAD_=BAM_CPAD,
-    BAM_CBASE_MATCH=BAM_CEQUAL,
-    BAM_CBASE_MISMATCH=BAM_CDIFF
-};
-
-typedef bam1_t bam_seq_t;
-
-#include "cram/sam_header.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-bam_hdr_t *cram_header_to_bam(SAM_hdr *h);
-SAM_hdr *bam_header_to_cram(bam_hdr_t *h);
-
-int bam_construct_seq(bam_seq_t **bp, size_t extra_len,
-		      const char *qname, size_t qname_len,
-		      int flag,
-		      int rname,      // Ref ID
-		      int pos,
-		      int end,        // aligned start/end coords
-		      int mapq,
-		      uint32_t ncigar, const uint32_t *cigar,
-		      int mrnm,       // Mate Ref ID
-		      int mpos,
-		      int isize,
-		      int len,
-		      const char *seq,
-		      const char *qual);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _CRAM_SAMTOOLS_H_ */