1 /*
2 Copyright (c) 2010-2013 Genome Research Ltd.
3 Author: James Bonfield <jkb@sanger.ac.uk>
4
5 Redistribution and use in source and binary forms, with or without
6 modification, are permitted provided that the following conditions are met:
7
8 1. Redistributions of source code must retain the above copyright notice,
9 this list of conditions and the following disclaimer.
10
11 2. Redistributions in binary form must reproduce the above copyright notice,
12 this list of conditions and the following disclaimer in the documentation
13 and/or other materials provided with the distribution.
14
15 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
16 Institute nor the names of its contributors may be used to endorse or promote
17 products derived from this software without specific prior written permission.
18
19 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
23 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 */
30
31 #include <config.h>
32
33 #include <assert.h>
34 #include <string.h>
35 #include <stdlib.h>
36
37 #include "cram/cram.h"
38 #include "htslib/sam.h"
39
40 /*---------------------------------------------------------------------------
41 * Samtools compatibility portion
42 */
bam_construct_seq(bam_seq_t ** bp,size_t extra_len,const char * qname,size_t qname_len,int flag,int rname,int pos,int end,int mapq,uint32_t ncigar,const uint32_t * cigar,int mrnm,int mpos,int isize,int len,const char * seq,const char * qual)43 int bam_construct_seq(bam_seq_t **bp, size_t extra_len,
44 const char *qname, size_t qname_len,
45 int flag,
46 int rname, // Ref ID
47 int pos,
48 int end, // aligned start/end coords
49 int mapq,
50 uint32_t ncigar, const uint32_t *cigar,
51 int mrnm, // Mate Ref ID
52 int mpos,
53 int isize,
54 int len,
55 const char *seq,
56 const char *qual) {
57 static const char L[256] = {
58 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
59 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
60 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
61 15,15,15,15,15,15,15,15,15,15,15,15,15, 0,15,15,
62 15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15,
63 15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15,
64 15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15,
65 15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15,
66 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
67 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
68 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
69 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
70 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
71 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
72 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
73 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15
74 };
75 bam1_t *b = (bam1_t *)*bp;
76 uint8_t *cp;
77 int i, qname_nuls, bam_len;
78
79 //b->l_aux = extra_len; // we fill this out later
80
81 qname_nuls = 4 - qname_len%4;
82 if (qname_len + qname_nuls > 255) // Check for core.l_qname overflow
83 return -1;
84 bam_len = qname_len + qname_nuls + ncigar*4 + (len+1)/2 + len + extra_len;
85 if (b->m_data < bam_len) {
86 b->m_data = bam_len;
87 kroundup32(b->m_data);
88 b->data = (uint8_t*)realloc(b->data, b->m_data);
89 if (!b->data)
90 return -1;
91 }
92 b->l_data = bam_len;
93
94 b->core.tid = rname;
95 b->core.pos = pos-1;
96 b->core.bin = bam_reg2bin(pos-1, end);
97 b->core.qual = mapq;
98 b->core.l_qname = qname_len+qname_nuls;
99 b->core.l_extranul = qname_nuls-1;
100 b->core.flag = flag;
101 b->core.n_cigar = ncigar;
102 b->core.l_qseq = len;
103 b->core.mtid = mrnm;
104 b->core.mpos = mpos-1;
105 b->core.isize = isize;
106
107 cp = b->data;
108
109 strncpy((char *)cp, qname, qname_len);
110 for (i = 0; i < qname_nuls; i++)
111 cp[qname_len+i] = '\0';
112 cp += qname_len+qname_nuls;
113 if (ncigar > 0) memcpy(cp, cigar, ncigar*4);
114 cp += ncigar*4;
115
116 for (i = 0; i+1 < len; i+=2) {
117 *cp++ = (L[(uc)seq[i]]<<4) + L[(uc)seq[i+1]];
118 }
119 if (i < len)
120 *cp++ = L[(uc)seq[i]]<<4;
121
122 if (qual)
123 memcpy(cp, qual, len);
124 else
125 memset(cp, '\xff', len);
126
127 return bam_len;
128 }
129
cram_header_to_bam(SAM_hdr * h)130 bam_hdr_t *cram_header_to_bam(SAM_hdr *h) {
131 int i;
132 bam_hdr_t *header = bam_hdr_init();
133
134 header->l_text = ks_len(&h->text);
135 header->text = malloc(header->l_text+1);
136 memcpy(header->text, ks_str(&h->text), header->l_text);
137 header->text[header->l_text] = 0;
138
139 header->n_targets = h->nref;
140 header->target_name = (char **)calloc(header->n_targets,
141 sizeof(char *));
142 header->target_len = (uint32_t *)calloc(header->n_targets, 4);
143
144 for (i = 0; i < h->nref; i++) {
145 header->target_name[i] = strdup(h->ref[i].name);
146 header->target_len[i] = h->ref[i].len;
147 }
148
149 return header;
150 }
151
bam_header_to_cram(bam_hdr_t * h)152 SAM_hdr *bam_header_to_cram(bam_hdr_t *h) {
153 return sam_hdr_parse_(h->text, h->l_text);
154 }
155