bcftools/vcf.c

   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
  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
  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
  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
  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         if (!has_ref) {
 106                 fprintf(v->fpout, "##SQ=");
 107                 for (i = 0; i < h->n_ref; ++i) {
 108                         fprintf(v->fpout, "%s", h->ns[i]);
 109                         fputc(i == h->n_ref - 1? '\n' : ',', v->fpout);
 110                 }
 111         }
 112         fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
 113         for (i = 0; i < h->n_smpl; ++i)
 114                 fprintf(v->fpout, "\t%s", h->sns[i]);
 115         fputc('\n', v->fpout);
 116         return 0;
 117 }
 118
 119 int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 120 {
 121         vcf_t *v = (vcf_t*)bp->v;
 122         extern void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s);
 123         if (!bp->is_vcf) return bcf_write(bp, h, b);
 124         bcf_fmt_core(h, b, &v->line);
 125         fwrite(v->line.s, 1, v->line.l, v->fpout);
 126         fputc('\n', v->fpout);
 127         return v->line.l + 1;
 128 }
 129
 130 int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 131 {
 132         int dret, k, i, sync = 0;
 133         vcf_t *v = (vcf_t*)bp->v;
 134         char *p, *q;
 135         kstring_t str, rn;
 136         ks_tokaux_t aux, a2;
 137         if (!bp->is_vcf) return bcf_read(bp, h, b);
 138         v->line.l = 0;
 139         str.l = 0; str.m = b->m_str; str.s = b->str;
 140         rn.l = rn.m = h->l_nm; rn.s = h->name;
 141         if (ks_getuntil(v->ks, '\n', &v->line, &dret) < 0) return -1;
 142         for (p = kstrtok(v->line.s, "\t", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
 143                 *(char*)aux.p = 0;
 144                 if (k == 0) { // ref
 145                         int tid = bcf_str2id(v->refhash, p);
 146                         if (tid < 0) {
 147                                 tid = bcf_str2id_add(v->refhash, p);
 148                                 kputs(p, &rn); kputc('\0', &rn);
 149                                 sync = 1;
 150                         }
 151                         b->tid = tid;
 152                 } else if (k == 1) { // pos
 153                         b->pos = atoi(p) - 1;
 154                 } else if (k == 5) { // qual
 155                         b->qual = (p[0] >= '0' && p[0] <= '9')? atof(p) : 0;
 156                 } else if (k <= 8) { // variable length strings
 157                         kputs(p, &str); kputc('\0', &str);
 158                         b->l_str = str.l; b->m_str = str.m; b->str = str.s;
 159                         if (k == 8) bcf_sync(h->n_smpl, b);
 160                 } else { // k > 9
 161                         if (strncmp(p, "./.", 3) == 0) {
 162                                 for (i = 0; i < b->n_gi; ++i) {
 163                                         if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
 164                                                 ((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
 165                                         } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
 166                                                 ((uint8_t*)b->gi[i].data)[k-9] = 0;
 167                                         } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
 168                                                 ((uint16_t*)b->gi[i].data)[k-9] = 0;
 169                                         } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
 170                                                 int y = b->n_alleles * (b->n_alleles + 1) / 2;
 171                                                 memset((uint8_t*)b->gi[i].data + (k - 9) * y, 0, y);
 172                                         } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
 173                                                 int y = b->n_alleles * (b->n_alleles + 1) / 2;
 174                                                 memset((float*)b->gi[i].data + (k - 9) * y, 0, y * 4);
 175                                         }
 176                                 }
 177                                 goto endblock;
 178                         }
 179                         for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
 180                                 if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
 181                                         ((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
 182                                 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
 183                                         double _x = strtod(q, &q);
 184                                         int x = (int)(_x + .499);
 185                                         if (x > 255) x = 255;
 186                                         ((uint8_t*)b->gi[i].data)[k-9] = x;
 187                                 } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
 188                                         int x = strtol(q, &q, 10);
 189                                         if (x > 0xffff) x = 0xffff;
 190                                         ((uint16_t*)b->gi[i].data)[k-9] = x;
 191                                 } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
 192                                         int x, y, j;
 193                                         uint8_t *data = (uint8_t*)b->gi[i].data;
 194                                         y = b->n_alleles * (b->n_alleles + 1) / 2;
 195                                         for (j = 0; j < y; ++j) {
 196                                                 x = strtol(q, &q, 10);
 197                                                 if (x > 255) x = 255;
 198                                                 data[(k-9) * y + j] = x;
 199                                                 ++q;
 200                                         }
 201                                 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
 202                                         int j, y;
 203                                         float x, *data = (float*)b->gi[i].data;
 204                                         y = b->n_alleles * (b->n_alleles + 1) / 2;
 205                                         for (j = 0; j < y; ++j) {
 206                                                 x = strtod(q, &q);
 207                                                 data[(k-9) * y + j] = x;
 208                                                 ++q;
 209                                         }
 210                                 }
 211                         }
 212                 endblock: i = i;
 213                 }
 214         }
 215         h->l_nm = rn.l; h->name = rn.s;
 216         if (sync) bcf_hdr_sync(h);
 217         return v->line.l + 1;
 218 }