1 #include <zlib.h>
2 #include <stdlib.h>
3 #include <stdio.h>
4 #include <string.h>
5 #include "bcf.h"
6 #include "kstring.h"
7 #include "kseq.h"
8 KSTREAM_INIT(gzFile, gzread, 4096)
9
10 typedef struct {
11 gzFile fp;
12 FILE *fpout;
13 kstream_t *ks;
14 void *refhash;
15 kstring_t line;
16 int max_ref;
17 } vcf_t;
18
vcf_hdr_read(bcf_t * bp)19 bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
20 {
21 kstring_t meta, smpl;
22 int dret;
23 vcf_t *v;
24 bcf_hdr_t *h;
25 if (!bp->is_vcf) return bcf_hdr_read(bp);
26 h = calloc(1, sizeof(bcf_hdr_t));
27 v = (vcf_t*)bp->v;
28 v->line.l = 0;
29 memset(&meta, 0, sizeof(kstring_t));
30 memset(&smpl, 0, sizeof(kstring_t));
31 while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) {
32 if (v->line.l < 2) continue;
33 if (v->line.s[0] != '#') return 0; // no sample line
34 if (v->line.s[0] == '#' && v->line.s[1] == '#') {
35 kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
36 } else if (v->line.s[0] == '#') {
37 int k;
38 ks_tokaux_t aux;
39 char *p;
40 for (p = kstrtok(v->line.s, "\t\n", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
41 if (k >= 9) {
42 kputsn(p, aux.p - p, &smpl);
43 kputc('\0', &smpl);
44 }
45 }
46 break;
47 }
48 }
49 kputc('\0', &meta);
50 h->name = 0;
51 h->sname = smpl.s; h->l_smpl = smpl.l;
52 h->txt = meta.s; h->l_txt = meta.l;
53 bcf_hdr_sync(h);
54 return h;
55 }
56
vcf_open(const char * fn,const char * mode)57 bcf_t *vcf_open(const char *fn, const char *mode)
58 {
59 bcf_t *bp;
60 vcf_t *v;
61 if (strchr(mode, 'b')) return bcf_open(fn, mode);
62 bp = calloc(1, sizeof(bcf_t));
63 v = calloc(1, sizeof(vcf_t));
64 bp->is_vcf = 1;
65 bp->v = v;
66 v->refhash = bcf_str2id_init();
67 if (strchr(mode, 'r')) {
68 v->fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
69 v->ks = ks_init(v->fp);
70 } else if (strchr(mode, 'w'))
71 v->fpout = strcmp(fn, "-")? fopen(fn, "w") : stdout;
72 return bp;
73 }
74
vcf_close(bcf_t * bp)75 int vcf_close(bcf_t *bp)
76 {
77 vcf_t *v;
78 if (bp == 0) return -1;
79 if (!bp->is_vcf) return bcf_close(bp);
80 v = (vcf_t*)bp->v;
81 if (v->fp) {
82 ks_destroy(v->ks);
83 gzclose(v->fp);
84 }
85 if (v->fpout) fclose(v->fpout);
86 free(v->line.s);
87 bcf_str2id_destroy(v->refhash);
88 free(v);
89 free(bp);
90 return 0;
91 }
92
vcf_hdr_write(bcf_t * bp,const bcf_hdr_t * h)93 int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
94 {
95 vcf_t *v = (vcf_t*)bp->v;
96 int i, has_ref = 0, has_ver = 0;
97 if (!bp->is_vcf) return bcf_hdr_write(bp, h);
98 if (h->l_txt > 0) {
99 if (strstr(h->txt, "##fileformat=")) has_ver = 1;
100 if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
101 fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
102 if (strstr(h->txt, "##SQ=")) has_ref = 1;
103 }
104 if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
105 fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
106 for (i = 0; i < h->n_smpl; ++i)
107 fprintf(v->fpout, "\t%s", h->sns[i]);
108 fputc('\n', v->fpout);
109 return 0;
110 }
111
vcf_write(bcf_t * bp,bcf_hdr_t * h,bcf1_t * b)112 int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
113 {
114 vcf_t *v = (vcf_t*)bp->v;
115 extern void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s);
116 if (!bp->is_vcf) return bcf_write(bp, h, b);
117 bcf_fmt_core(h, b, &v->line);
118 fwrite(v->line.s, 1, v->line.l, v->fpout);
119 fputc('\n', v->fpout);
120 return v->line.l + 1;
121 }
122
vcf_read(bcf_t * bp,bcf_hdr_t * h,bcf1_t * b)123 int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
124 {
125 int dret, k, i, sync = 0;
126 vcf_t *v = (vcf_t*)bp->v;
127 char *p, *q;
128 kstring_t str, rn;
129 ks_tokaux_t aux, a2;
130 if (!bp->is_vcf) return bcf_read(bp, h, b);
131 v->line.l = 0;
132 str.l = 0; str.m = b->m_str; str.s = b->str;
133 rn.l = rn.m = h->l_nm; rn.s = h->name;
134 if (ks_getuntil(v->ks, '\n', &v->line, &dret) < 0) return -1;
135 b->n_smpl = h->n_smpl;
136 for (p = kstrtok(v->line.s, "\t", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
137 *(char*)aux.p = 0;
138 if (k == 0) { // ref
139 int tid = bcf_str2id(v->refhash, p);
140 if (tid < 0) {
141 tid = bcf_str2id_add(v->refhash, p);
142 kputs(p, &rn); kputc('\0', &rn);
143 sync = 1;
144 }
145 b->tid = tid;
146 } else if (k == 1) { // pos
147 b->pos = atoi(p) - 1;
148 } else if (k == 5) { // qual
149 b->qual = (p[0] >= '0' && p[0] <= '9')? atof(p) : 0;
150 } else if (k <= 8) { // variable length strings
151 kputs(p, &str); kputc('\0', &str);
152 b->l_str = str.l; b->m_str = str.m; b->str = str.s;
153 if (k == 8) bcf_sync(b);
154 } else { // k > 9
155 if (strncmp(p, "./.", 3) == 0) {
156 for (i = 0; i < b->n_gi; ++i) {
157 if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
158 ((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
159 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
160 ((uint8_t*)b->gi[i].data)[k-9] = 0;
161 } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
162 ((uint16_t*)b->gi[i].data)[k-9] = 0;
163 } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
164 int y = b->n_alleles * (b->n_alleles + 1) / 2;
165 memset((uint8_t*)b->gi[i].data + (k - 9) * y, 0, y);
166 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
167 int y = b->n_alleles * (b->n_alleles + 1) / 2;
168 memset((float*)b->gi[i].data + (k - 9) * y, 0, y * 4);
169 }
170 }
171 goto endblock;
172 }
173 for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
174 if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
175 ((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
176 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
177 double _x = strtod(q, &q);
178 int x = (int)(_x + .499);
179 if (x > 255) x = 255;
180 ((uint8_t*)b->gi[i].data)[k-9] = x;
181 } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
182 int x = strtol(q, &q, 10);
183 if (x > 0xffff) x = 0xffff;
184 ((uint16_t*)b->gi[i].data)[k-9] = x;
185 } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
186 int x, y, j;
187 uint8_t *data = (uint8_t*)b->gi[i].data;
188 y = b->n_alleles * (b->n_alleles + 1) / 2;
189 for (j = 0; j < y; ++j) {
190 x = strtol(q, &q, 10);
191 if (x > 255) x = 255;
192 data[(k-9) * y + j] = x;
193 ++q;
194 }
195 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
196 int j, y;
197 float x, *data = (float*)b->gi[i].data;
198 y = b->n_alleles * (b->n_alleles + 1) / 2;
199 for (j = 0; j < y; ++j) {
200 x = strtod(q, &q);
201 data[(k-9) * y + j] = x;
202 ++q;
203 }
204 }
205 }
206 endblock: i = i;
207 }
208 }
209 h->l_nm = rn.l; h->name = rn.s;
210 if (sync) bcf_hdr_sync(h);
211 return v->line.l + 1;
212 }
213