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1 /*
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2 Copyright (c) 2010-2013 Genome Research Ltd.
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3 Author: James Bonfield <jkb@sanger.ac.uk>
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4
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5 Redistribution and use in source and binary forms, with or without
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6 modification, are permitted provided that the following conditions are met:
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7
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8 1. Redistributions of source code must retain the above copyright notice,
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9 this list of conditions and the following disclaimer.
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10
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11 2. Redistributions in binary form must reproduce the above copyright notice,
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12 this list of conditions and the following disclaimer in the documentation
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13 and/or other materials provided with the distribution.
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14
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15 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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16 Institute nor the names of its contributors may be used to endorse or promote
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17 products derived from this software without specific prior written permission.
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18
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19 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
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20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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22 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
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23 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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24 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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29 */
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30
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31 #include <assert.h>
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32 #include <string.h>
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33 #include <stdlib.h>
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34
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35 #include "cram/cram.h"
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36 #include "htslib/sam.h"
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37
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38 /*---------------------------------------------------------------------------
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39 * Samtools compatibility portion
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40 */
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41 int bam_construct_seq(bam_seq_t **bp, size_t extra_len,
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42 const char *qname, size_t qname_len,
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43 int flag,
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44 int rname, // Ref ID
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45 int pos,
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46 int end, // aligned start/end coords
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47 int mapq,
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48 uint32_t ncigar, const uint32_t *cigar,
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49 int mrnm, // Mate Ref ID
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50 int mpos,
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51 int isize,
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52 int len,
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53 const char *seq,
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54 const char *qual) {
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55 static const char L[256] = {
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56 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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57 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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58 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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59 15,15,15,15,15,15,15,15,15,15,15,15,15, 0,15,15,
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60 15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15,
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61 15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15,
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62 15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15,
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63 15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15,
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64 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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65 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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66 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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67 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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68 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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69 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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70 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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71 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15
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72 };
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73 bam1_t *b = (bam1_t *)*bp;
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74 uint8_t *cp;
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75 int i, bam_len;
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76
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77 //b->l_aux = extra_len; // we fill this out later
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78
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79 bam_len = qname_len + 1 + ncigar*4 + (len+1)/2 + len + extra_len;
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80 if (b->m_data < bam_len) {
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81 b->m_data = bam_len;
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82 kroundup32(b->m_data);
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83 b->data = (uint8_t*)realloc(b->data, b->m_data);
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84 if (!b->data)
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85 return -1;
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86 }
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87 b->l_data = bam_len;
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88
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89 b->core.tid = rname;
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90 b->core.pos = pos-1;
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91 b->core.bin = bam_reg2bin(pos, end);
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92 b->core.qual = mapq;
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93 b->core.l_qname = qname_len+1;
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94 b->core.flag = flag;
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95 b->core.n_cigar = ncigar;
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96 b->core.l_qseq = len;
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97 b->core.mtid = mrnm;
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98 b->core.mpos = mpos-1;
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99 b->core.isize = isize;
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100
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101 cp = b->data;
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102
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103 strncpy((char *)cp, qname, qname_len);
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104 cp[qname_len] = 0;
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105 cp += qname_len+1;
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106 memcpy(cp, cigar, ncigar*4);
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107 cp += ncigar*4;
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108
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109 for (i = 0; i+1 < len; i+=2) {
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110 *cp++ = (L[(uc)seq[i]]<<4) + L[(uc)seq[i+1]];
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111 }
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112 if (i < len)
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113 *cp++ = L[(uc)seq[i]]<<4;
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114
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115 if (qual)
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116 memcpy(cp, qual, len);
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117 else
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118 memset(cp, '\xff', len);
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119
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120 return 0;
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121 }
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122
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123 bam_hdr_t *cram_header_to_bam(SAM_hdr *h) {
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124 int i;
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125 bam_hdr_t *header = bam_hdr_init();
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126
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127 header->l_text = ks_len(&h->text);
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128 header->text = malloc(header->l_text+1);
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129 memcpy(header->text, ks_str(&h->text), header->l_text);
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130 header->text[header->l_text] = 0;
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131
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132 header->n_targets = h->nref;
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133 header->target_name = (char **)calloc(header->n_targets,
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134 sizeof(char *));
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135 header->target_len = (uint32_t *)calloc(header->n_targets, 4);
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136
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137 for (i = 0; i < h->nref; i++) {
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138 header->target_name[i] = strdup(h->ref[i].name);
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139 header->target_len[i] = h->ref[i].len;
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140 }
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141
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142 return header;
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143 }
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144
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145 SAM_hdr *bam_header_to_cram(bam_hdr_t *h) {
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146 return sam_hdr_parse_(h->text, h->l_text);
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147 }
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