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comparison ezBAMQC/src/htslib/cram/cram_samtools.c @ 0:dfa3745e5fd8

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author youngkim
date Thu, 24 Mar 2016 17:12:52 -0400
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-1:000000000000 0:dfa3745e5fd8
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 <assert.h>
32 #include <string.h>
33 #include <stdlib.h>
34
35 #include "cram/cram.h"
36 #include "htslib/sam.h"
37
38 /*---------------------------------------------------------------------------
39 * Samtools compatibility portion
40 */
41 int bam_construct_seq(bam_seq_t **bp, size_t extra_len,
42 const char *qname, size_t qname_len,
43 int flag,
44 int rname, // Ref ID
45 int pos,
46 int end, // aligned start/end coords
47 int mapq,
48 uint32_t ncigar, const uint32_t *cigar,
49 int mrnm, // Mate Ref ID
50 int mpos,
51 int isize,
52 int len,
53 const char *seq,
54 const char *qual) {
55 static const char L[256] = {
56 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
57 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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, 0,15,15,
60 15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15,
61 15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15,
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 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
65 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
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 };
73 bam1_t *b = (bam1_t *)*bp;
74 uint8_t *cp;
75 int i, bam_len;
76
77 //b->l_aux = extra_len; // we fill this out later
78
79 bam_len = qname_len + 1 + ncigar*4 + (len+1)/2 + len + extra_len;
80 if (b->m_data < bam_len) {
81 b->m_data = bam_len;
82 kroundup32(b->m_data);
83 b->data = (uint8_t*)realloc(b->data, b->m_data);
84 if (!b->data)
85 return -1;
86 }
87 b->l_data = bam_len;
88
89 b->core.tid = rname;
90 b->core.pos = pos-1;
91 b->core.bin = bam_reg2bin(pos, end);
92 b->core.qual = mapq;
93 b->core.l_qname = qname_len+1;
94 b->core.flag = flag;
95 b->core.n_cigar = ncigar;
96 b->core.l_qseq = len;
97 b->core.mtid = mrnm;
98 b->core.mpos = mpos-1;
99 b->core.isize = isize;
100
101 cp = b->data;
102
103 strncpy((char *)cp, qname, qname_len);
104 cp[qname_len] = 0;
105 cp += qname_len+1;
106 memcpy(cp, cigar, ncigar*4);
107 cp += ncigar*4;
108
109 for (i = 0; i+1 < len; i+=2) {
110 *cp++ = (L[(uc)seq[i]]<<4) + L[(uc)seq[i+1]];
111 }
112 if (i < len)
113 *cp++ = L[(uc)seq[i]]<<4;
114
115 if (qual)
116 memcpy(cp, qual, len);
117 else
118 memset(cp, '\xff', len);
119
120 return 0;
121 }
122
123 bam_hdr_t *cram_header_to_bam(SAM_hdr *h) {
124 int i;
125 bam_hdr_t *header = bam_hdr_init();
126
127 header->l_text = ks_len(&h->text);
128 header->text = malloc(header->l_text+1);
129 memcpy(header->text, ks_str(&h->text), header->l_text);
130 header->text[header->l_text] = 0;
131
132 header->n_targets = h->nref;
133 header->target_name = (char **)calloc(header->n_targets,
134 sizeof(char *));
135 header->target_len = (uint32_t *)calloc(header->n_targets, 4);
136
137 for (i = 0; i < h->nref; i++) {
138 header->target_name[i] = strdup(h->ref[i].name);
139 header->target_len[i] = h->ref[i].len;
140 }
141
142 return header;
143 }
144
145 SAM_hdr *bam_header_to_cram(bam_hdr_t *h) {
146 return sam_hdr_parse_(h->text, h->l_text);
147 }