samtools/bcftools/vcf.c.pysam.c

   1 #include "pysam.h"
   2
   3 #include <zlib.h>
   4 #include <stdlib.h>
   5 #include <stdio.h>
   6 #include <string.h>
   7 #include "bcf.h"
   8 #include "kstring.h"
   9 #include "kseq.h"
  10 KSTREAM_INIT(gzFile, gzread, 4096)
  11
  12 typedef struct {
  13         gzFile fp;
  14         FILE *fpout;
  15         kstream_t *ks;
  16         void *refhash;
  17         kstring_t line;
  18         int max_ref;
  19 } vcf_t;
  20
  21 bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
  22 {
  23         kstring_t meta, smpl;
  24         int dret;
  25         vcf_t *v;
  26         bcf_hdr_t *h;
  27         if (!bp->is_vcf) return bcf_hdr_read(bp);
  28         h = calloc(1, sizeof(bcf_hdr_t));
  29         v = (vcf_t*)bp->v;
  30         v->line.l = 0;
  31         memset(&meta, 0, sizeof(kstring_t));
  32         memset(&smpl, 0, sizeof(kstring_t));
  33         while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) {
  34                 if (v->line.l < 2) continue;
  35                 if (v->line.s[0] != '#') return 0; // no sample line
  36                 if (v->line.s[0] == '#' && v->line.s[1] == '#') {
  37                         kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
  38                 } else if (v->line.s[0] == '#') {
  39                         int k;
  40                         ks_tokaux_t aux;
  41                         char *p;
  42                         for (p = kstrtok(v->line.s, "\t\n", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
  43                                 if (k >= 9) {
  44                                         kputsn(p, aux.p - p, &smpl);
  45                                         kputc('\0', &smpl);
  46                                 }
  47                         }
  48                         break;
  49                 }
  50         }
  51         kputc('\0', &meta);
  52         h->name = 0;
  53         h->sname = smpl.s; h->l_smpl = smpl.l;
  54         h->txt = meta.s; h->l_txt = meta.l;
  55         bcf_hdr_sync(h);
  56         return h;
  57 }
  58
  59 bcf_t *vcf_open(const char *fn, const char *mode)
  60 {
  61         bcf_t *bp;
  62         vcf_t *v;
  63         if (strchr(mode, 'b')) return bcf_open(fn, mode);
  64         bp = calloc(1, sizeof(bcf_t));
  65         v = calloc(1, sizeof(vcf_t));
  66         bp->is_vcf = 1;
  67         bp->v = v;
  68         v->refhash = bcf_str2id_init();
  69         if (strchr(mode, 'r')) {
  70                 v->fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
  71                 v->ks = ks_init(v->fp);
  72         } else if (strchr(mode, 'w'))
  73                 v->fpout = strcmp(fn, "-")? fopen(fn, "w") : stdout;
  74         return bp;
  75 }
  76
  77 int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn)
  78 {
  79         vcf_t *v;
  80         gzFile fp;
  81         kstream_t *ks;
  82         kstring_t s, rn;
  83         int dret;
  84         if (bp == 0) return -1;
  85         if (!bp->is_vcf) return 0;
  86         s.l = s.m = 0; s.s = 0;
  87         rn.m = rn.l = h->l_nm; rn.s = h->name;
  88         v = (vcf_t*)bp->v;
  89         fp = gzopen(fn, "r");
  90         ks = ks_init(fp);
  91         while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
  92                 bcf_str2id_add(v->refhash, strdup(s.s));
  93                 kputs(s.s, &rn); kputc('\0', &rn);
  94                 if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
  95         }
  96         ks_destroy(ks);
  97         gzclose(fp);
  98         h->l_nm = rn.l; h->name = rn.s;
  99         bcf_hdr_sync(h);
 100         free(s.s);
 101         return 0;
 102 }
 103
 104 int vcf_close(bcf_t *bp)
 105 {
 106         vcf_t *v;
 107         if (bp == 0) return -1;
 108         if (!bp->is_vcf) return bcf_close(bp);
 109         v = (vcf_t*)bp->v;
 110         if (v->fp) {
 111                 ks_destroy(v->ks);
 112                 gzclose(v->fp);
 113         }
 114         if (v->fpout) fclose(v->fpout);
 115         free(v->line.s);
 116         bcf_str2id_thorough_destroy(v->refhash);
 117         free(v);
 118         free(bp);
 119         return 0;
 120 }
 121
 122 int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
 123 {
 124         vcf_t *v = (vcf_t*)bp->v;
 125         int i, has_ver = 0;
 126         if (!bp->is_vcf) return bcf_hdr_write(bp, h);
 127         if (h->l_txt > 0) {
 128                 if (strstr(h->txt, "##fileformat=")) has_ver = 1;
 129                 if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
 130                 fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
 131         }
 132         if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
 133         fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
 134         for (i = 0; i < h->n_smpl; ++i)
 135                 fprintf(v->fpout, "\t%s", h->sns[i]);
 136         fputc('\n', v->fpout);
 137         return 0;
 138 }
 139
 140 int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 141 {
 142         vcf_t *v = (vcf_t*)bp->v;
 143         extern void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s);
 144         if (!bp->is_vcf) return bcf_write(bp, h, b);
 145         bcf_fmt_core(h, b, &v->line);
 146         fwrite(v->line.s, 1, v->line.l, v->fpout);
 147         fputc('\n', v->fpout);
 148         return v->line.l + 1;
 149 }
 150
 151 int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 152 {
 153         int dret, k, i, sync = 0;
 154         vcf_t *v = (vcf_t*)bp->v;
 155         char *p, *q;
 156         kstring_t str, rn;
 157         ks_tokaux_t aux, a2;
 158         if (!bp->is_vcf) return bcf_read(bp, h, b);
 159         v->line.l = 0;
 160         str.l = 0; str.m = b->m_str; str.s = b->str;
 161         rn.l = rn.m = h->l_nm; rn.s = h->name;
 162         if (ks_getuntil(v->ks, '\n', &v->line, &dret) < 0) return -1;
 163         b->n_smpl = h->n_smpl;
 164         for (p = kstrtok(v->line.s, "\t", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
 165                 *(char*)aux.p = 0;
 166                 if (k == 0) { // ref
 167                         int tid = bcf_str2id(v->refhash, p);
 168                         if (tid < 0) {
 169                                 tid = bcf_str2id_add(v->refhash, strdup(p));
 170                                 kputs(p, &rn); kputc('\0', &rn);
 171                                 sync = 1;
 172                         }
 173                         b->tid = tid;
 174                 } else if (k == 1) { // pos
 175                         b->pos = atoi(p) - 1;
 176                 } else if (k == 5) { // qual
 177                         b->qual = (p[0] >= '0' && p[0] <= '9')? atof(p) : 0;
 178                 } else if (k <= 8) { // variable length strings
 179                         kputs(p, &str); kputc('\0', &str);
 180                         b->l_str = str.l; b->m_str = str.m; b->str = str.s;
 181                         if (k == 8) bcf_sync(b);
 182                 } else { // k > 9
 183                         if (strncmp(p, "./.", 3) == 0) {
 184                                 for (i = 0; i < b->n_gi; ++i) {
 185                                         if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
 186                                                 ((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
 187                                         } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
 188                                                 ((uint8_t*)b->gi[i].data)[k-9] = 0;
 189                                         } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
 190                                                 ((int32_t*)b->gi[i].data)[k-9] = 0;
 191                                         } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
 192                                                 ((uint16_t*)b->gi[i].data)[k-9] = 0;
 193                                         } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
 194                                                 int y = b->n_alleles * (b->n_alleles + 1) / 2;
 195                                                 memset((uint8_t*)b->gi[i].data + (k - 9) * y, 0, y);
 196                                         } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
 197                                                 int y = b->n_alleles * (b->n_alleles + 1) / 2;
 198                                                 memset((float*)b->gi[i].data + (k - 9) * y, 0, y * 4);
 199                                         }
 200                                 }
 201                                 goto endblock;
 202                         }
 203                         for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
 204                                 if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
 205                                         ((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
 206                                 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
 207                                         double _x = strtod(q, &q);
 208                                         int x = (int)(_x + .499);
 209                                         if (x > 255) x = 255;
 210                                         ((uint8_t*)b->gi[i].data)[k-9] = x;
 211                                 } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
 212                                         int x = strtol(q, &q, 10);
 213                                         if (x > 0xffff) x = 0xffff;
 214                                         ((uint32_t*)b->gi[i].data)[k-9] = x;
 215                                 } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
 216                                         int x = strtol(q, &q, 10);
 217                                         if (x > 0xffff) x = 0xffff;
 218                                         ((uint16_t*)b->gi[i].data)[k-9] = x;
 219                                 } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
 220                                         int x, y, j;
 221                                         uint8_t *data = (uint8_t*)b->gi[i].data;
 222                                         y = b->n_alleles * (b->n_alleles + 1) / 2;
 223                                         for (j = 0; j < y; ++j) {
 224                                                 x = strtol(q, &q, 10);
 225                                                 if (x > 255) x = 255;
 226                                                 data[(k-9) * y + j] = x;
 227                                                 ++q;
 228                                         }
 229                                 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
 230                                         int j, y;
 231                                         float x, *data = (float*)b->gi[i].data;
 232                                         y = b->n_alleles * (b->n_alleles + 1) / 2;
 233                                         for (j = 0; j < y; ++j) {
 234                                                 x = strtod(q, &q);
 235                                                 data[(k-9) * y + j] = x > 0? -x/10. : x;
 236                                                 ++q;
 237                                         }
 238                                 }
 239                         }
 240                 endblock: i = i;
 241                 }
 242         }
 243         h->l_nm = rn.l; h->name = rn.s;
 244         if (sync) bcf_hdr_sync(h);
 245         return v->line.l + 1;
 246 }