7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/cram/cram_samtools.c src/htslib/cram/cram_samtools.c deleted file mode 100644 index 9e95c7b793d..00000000000 --- src/htslib/cram/cram_samtools.c +++ /dev/null @@ -1,149 +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. -*/ - -#include <config.h> - -#include <assert.h> -#include <string.h> -#include <stdlib.h> - -#include "cram/cram.h" -#include "htslib/sam.h" - -/*--------------------------------------------------------------------------- - * Samtools compatibility portion - */ -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) { - static const char L[256] = { - 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, - 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, - 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, - 15,15,15,15,15,15,15,15,15,15,15,15,15, 0,15,15, - 15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15, - 15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15, - 15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15, - 15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15, - 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, - 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, - 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, - 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, - 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, - 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, - 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, - 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15 - }; - bam1_t *b = (bam1_t *)*bp; - uint8_t *cp; - int i, bam_len; - - //b->l_aux = extra_len; // we fill this out later - - bam_len = qname_len + 1 + ncigar*4 + (len+1)/2 + len + extra_len; - if (b->m_data < bam_len) { - b->m_data = bam_len; - kroundup32(b->m_data); - b->data = (uint8_t*)realloc(b->data, b->m_data); - if (!b->data) - return -1; - } - b->l_data = bam_len; - - b->core.tid = rname; - b->core.pos = pos-1; - b->core.bin = bam_reg2bin(pos, end); - b->core.qual = mapq; - b->core.l_qname = qname_len+1; - b->core.flag = flag; - b->core.n_cigar = ncigar; - b->core.l_qseq = len; - b->core.mtid = mrnm; - b->core.mpos = mpos-1; - b->core.isize = isize; - - cp = b->data; - - strncpy((char *)cp, qname, qname_len); - cp[qname_len] = 0; - cp += qname_len+1; - memcpy(cp, cigar, ncigar*4); - cp += ncigar*4; - - for (i = 0; i+1 < len; i+=2) { - *cp++ = (L[(uc)seq[i]]<<4) + L[(uc)seq[i+1]]; - } - if (i < len) - *cp++ = L[(uc)seq[i]]<<4; - - if (qual) - memcpy(cp, qual, len); - else - memset(cp, '\xff', len); - - return 0; -} - -bam_hdr_t *cram_header_to_bam(SAM_hdr *h) { - int i; - bam_hdr_t *header = bam_hdr_init(); - - header->l_text = ks_len(&h->text); - header->text = malloc(header->l_text+1); - memcpy(header->text, ks_str(&h->text), header->l_text); - header->text[header->l_text] = 0; - - header->n_targets = h->nref; - header->target_name = (char **)calloc(header->n_targets, - sizeof(char *)); - header->target_len = (uint32_t *)calloc(header->n_targets, 4); - - for (i = 0; i < h->nref; i++) { - header->target_name[i] = strdup(h->ref[i].name); - header->target_len[i] = h->ref[i].len; - } - - return header; -} - -SAM_hdr *bam_header_to_cram(bam_hdr_t *h) { - return sam_hdr_parse_(h->text, h->l_text); -}