text: /*
  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 <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;
  
      memcpy(cp, qual, 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);
  }
  