else kputs(p, s);
}
-char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
+void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
{
- kstring_t s;
int i, j, x;
- memset(&s, 0, sizeof(kstring_t));
- kputs(h->ns[b->tid], &s); kputc('\t', &s);
- kputw(b->pos + 1, &s); kputc('\t', &s);
- fmt_str(b->str, &s); kputc('\t', &s);
- fmt_str(b->ref, &s); kputc('\t', &s);
- fmt_str(b->alt, &s); kputc('\t', &s);
- kputw(b->qual, &s); kputc('\t', &s);
- fmt_str(b->flt, &s); kputc('\t', &s);
- fmt_str(b->info, &s);
+ s->l = 0;
+ kputs(h->ns[b->tid], s); kputc('\t', s);
+ kputw(b->pos + 1, s); kputc('\t', s);
+ fmt_str(b->str, s); kputc('\t', s);
+ fmt_str(b->ref, s); kputc('\t', s);
+ fmt_str(b->alt, s); kputc('\t', s);
+ kputw(b->qual, s); kputc('\t', s);
+ fmt_str(b->flt, s); kputc('\t', s);
+ fmt_str(b->info, s);
if (b->fmt[0]) {
- kputc('\t', &s);
- fmt_str(b->fmt, &s);
+ kputc('\t', s);
+ fmt_str(b->fmt, s);
}
x = b->n_alleles * (b->n_alleles + 1) / 2;
for (j = 0; j < h->n_smpl; ++j) {
- kputc('\t', &s);
+ kputc('\t', s);
for (i = 0; i < b->n_gi; ++i) {
- if (i) kputc(':', &s);
+ if (i) kputc(':', s);
if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
int k;
for (k = 0; k < x; ++k) {
- if (k > 0) kputc(',', &s);
- kputw(d[k], &s);
+ if (k > 0) kputc(',', s);
+ kputw(d[k], s);
}
} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
- kputw(((uint16_t*)b->gi[i].data)[j], &s);
+ kputw(((uint16_t*)b->gi[i].data)[j], s);
} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
- kputw(((uint8_t*)b->gi[i].data)[j], &s);
+ kputw(((uint8_t*)b->gi[i].data)[j], s);
+ } else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
+ int y = ((uint8_t*)b->gi[i].data)[j];
+ kputc('0' + (y>>3&7), s);
+ kputc("/|"[y>>6&1], s);
+ kputc('0' + (y&7), s);
}
}
}
+}
+
+char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
+{
+ kstring_t s;
+ s.l = s.m = 0; s.s = 0;
+ bcf_fmt_core(h, b, &s);
return s.s;
}
int bcf_destroy(bcf1_t *b);
char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b);
+ bcf_t *vcf_open(const char *fn, const char *mode);
int vcf_close(bcf_t *bp);
+ bcf_hdr_t *vcf_hdr_read(bcf_t *bp);
+ int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h);
+ int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
+ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
void *bcf_build_refhash(bcf_hdr_t *h);
void bcf_str2id_destroy(void *_hash);
+ int bcf_str2id_add(void *_hash, const char *str);
int bcf_str2id(void *_hash, const char *str);
+ void *bcf_str2id_init();
int bcf_idx_build(const char *fn);
uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg, int end);
return kh_init(str2id);
}
-int bcf_str2id_put(void *_hash, const char *str, int id)
-{
- return 0;
-}
-
void bcf_str2id_destroy(void *_hash)
{
khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
return k == kh_end(hash)? -1 : kh_val(hash, k);
}
+int bcf_str2id_add(void *_hash, const char *str)
+{
+ khint_t k;
+ int ret;
+ khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+ if (!hash) return -1;
+ k = kh_put(str2id, hash, str, &ret);
+ if (ret == 0) return kh_val(hash, k);
+ kh_val(hash, k) = kh_size(hash) - 1;
+ return kh_val(hash, k);
+}
int bcfview(int argc, char *argv[]);
int bcf_main_index(int argc, char *argv[]);
-int vcf_test(int argc, char *argv[]);
int main(int argc, char *argv[])
{
}
if (strcmp(argv[1], "view") == 0) return bcfview(argc-1, argv+1);
if (strcmp(argv[1], "index") == 0) return bcf_main_index(argc-1, argv+1);
- if (strcmp(argv[1], "test") == 0) return vcf_test(argc-1, argv+1);
else {
fprintf(stderr, "[main] Unrecognized command.\n");
return 1;
int dret;
vcf_t *v;
bcf_hdr_t *h;
- if (!bp->is_vcf) return 0;
+ if (!bp->is_vcf) return bcf_hdr_read(bp);
h = calloc(1, sizeof(bcf_hdr_t));
v = (vcf_t*)bp->v;
v->line.l = 0;
kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
} else if (v->line.s[0] == '#') {
int k;
- char *p, *q, *r;
- for (q = v->line.s, p = q + 1, k = 0; *p; ++p) {
- if (*p == '\t' || *(p+1) == 0) {
- r = *(p+1) == 0? p+1 : p;
- if (k >= 9) {
- kputsn(q, r - q, &smpl);
- kputc('\0', &smpl);
- }
- q = p + 1; ++k;
+ ks_tokaux_t aux;
+ char *p;
+ for (p = kstrtok(v->line.s, "\t\n", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
+ if (k >= 9) {
+ kputsn(p, aux.p - p, &smpl);
+ kputc('\0', &smpl);
}
}
break;
{
bcf_t *bp;
vcf_t *v;
+ if (strchr(mode, 'b')) return bcf_open(fn, mode);
bp = calloc(1, sizeof(bcf_t));
v = calloc(1, sizeof(vcf_t));
bp->is_vcf = 1;
bp->v = v;
+ v->refhash = bcf_str2id_init();
if (strchr(mode, 'r')) {
v->fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
v->ks = ks_init(v->fp);
} else if (strchr(mode, 'w'))
- v->fpout = strcmp(fn, "-")? fopen(fn, "w") : fdopen(fileno(stdout), "w");
+ v->fpout = strcmp(fn, "-")? fopen(fn, "w") : stdout;
return bp;
}
-void bcf_hdr_clear(bcf_hdr_t *b);
-
int vcf_close(bcf_t *bp)
{
vcf_t *v;
if (bp == 0) return -1;
- if (bp->v == 0) return -1;
+ if (!bp->is_vcf) return bcf_close(bp);
v = (vcf_t*)bp->v;
if (v->fp) {
ks_destroy(v->ks);
}
if (v->fpout) fclose(v->fpout);
free(v->line.s);
+ bcf_str2id_destroy(v->refhash);
free(v);
free(bp);
return 0;
{
vcf_t *v = (vcf_t*)bp->v;
int i;
- if (v == 0 || v->fpout == 0) return -1;
- fwrite(h->txt, 1, h->l_txt, v->fpout);
- fprintf(v->fpout, "#CHROM\tPOS\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
+ if (!bp->is_vcf) return bcf_hdr_write(bp, h);
+ if (h->l_txt > 0) fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
+ fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
for (i = 0; i < h->n_smpl; ++i)
fprintf(v->fpout, "\t%s", h->sns[i]);
fputc('\n', v->fpout);
return 0;
}
+int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
+{
+ vcf_t *v = (vcf_t*)bp->v;
+ extern void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s);
+ if (!bp->is_vcf) return bcf_write(bp, h, b);
+ bcf_fmt_core(h, b, &v->line);
+ fwrite(v->line.s, 1, v->line.l, v->fpout);
+ fputc('\n', v->fpout);
+ return v->line.l + 1;
+}
+
int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
{
- int dret, k;
+ int dret, k, i, sync = 0;
vcf_t *v = (vcf_t*)bp->v;
- char *p, *q, *r;
- kstring_t str;
+ char *p, *q;
+ kstring_t str, rn;
+ ks_tokaux_t aux, a2;
+ if (!bp->is_vcf) return bcf_read(bp, h, b);
v->line.l = 0;
str.l = 0; str.m = b->m_str; str.s = b->str;
+ rn.l = rn.m = h->l_nm; rn.s = h->name;
if (ks_getuntil(v->ks, '\n', &v->line, &dret) < 0) return -1;
- for (q = v->line.s, p = q + 1, k = 0; *p; ++p) {
- if (*p == '\t' || *(p+1) == '\0') {
- ++k;
- r = *(p+1)? p : p + 1;
- *r = '\0';
- if (k == 1) { // ref
- } else if (k == 2) {
- b->pos = atoi(q);
- } else if (k == 3 || k == 4 || k == 5 || k == 7 || k == 8 || k == 9) {
- kputsn(q, r - q + 1, &str);
- if (k == 9) bcf_sync(h->n_smpl, b);
- } else if (k == 6) {
- b->qual = (q[0] >= '0' && q[0] <= '9')? atoi(q) : 0;
+ for (p = kstrtok(v->line.s, "\t", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
+ *(char*)aux.p = 0;
+ if (k == 0) { // ref
+ int tid = bcf_str2id(v->refhash, p);
+ if (tid < 0) {
+ tid = bcf_str2id_add(v->refhash, p);
+ kputs(p, &rn);
+ sync = 1;
+ }
+ b->tid = tid;
+ } else if (k == 1) { // pos
+ b->pos = atoi(p);
+ } else if (k == 5) { // qual
+ b->qual = (p[0] >= '0' && p[0] <= '9')? atoi(p) : 0;
+ } else if (k <= 8) { // variable length strings
+ kputs(p, &str); kputc('\0', &str);
+ b->l_str = str.l; b->m_str = str.m; b->str = str.s;
+ if (k == 8) bcf_sync(h->n_smpl, b);
+ } else {
+ for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
+ if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
+ ((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
+ int x = strtol(q, &q, 10);
+ if (x > 255) x = 255;
+ ((uint8_t*)b->gi[i].data)[k-9] = x;
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+ int x = strtol(q, &q, 10);
+ if (x > 0xffff) x = 0xffff;
+ ((uint16_t*)b->gi[i].data)[k-9] = x;
+ }
}
- q = p + 1;
}
}
+ h->l_nm = rn.l; h->name = rn.s;
+ if (sync) bcf_hdr_sync(h);
return v->line.l + 1;
}
-
-int vcf_test(int argc, char *argv[])
-{
- bcf_t *bp, *bpout;
- bcf_hdr_t *h;
- bp = vcf_open(argv[1], "r");
- bpout = vcf_open("-", "w");
- h = vcf_hdr_read(bpout);
- vcf_hdr_write(bpout, h);
- vcf_close(bp);
- return 0;
-}
#define VC_NO_PL 1
#define VC_NO_GENO 2
-#define VC_BCF 4
+#define VC_BCFOUT 4
#define VC_CALL 8
#define VC_VARONLY 16
+#define VC_VCFIN 32
+#define VC_UNCOMP 64
typedef struct {
int flag, prior_type;
bcf_p1aux_t *p1 = 0;
bcf_hdr_t *h;
int tid, begin, end;
+ char moder[4], modew[4];
khash_t(set64) *hash = 0;
tid = begin = end = -1;
memset(&vc, 0, sizeof(viewconf_t));
vc.prior_type = -1; vc.theta = 1e-3; vc.pref = 0.9;
- while ((c = getopt(argc, argv, "l:cGvLbP:t:p:")) >= 0) {
+ while ((c = getopt(argc, argv, "l:cGvLbSuP:t:p:")) >= 0) {
switch (c) {
case 'l': vc.fn_list = strdup(optarg); break;
case 'G': vc.flag |= VC_NO_GENO; break;
case 'L': vc.flag |= VC_NO_PL; break;
- case 'b': vc.flag |= VC_BCF; break;
+ case 'b': vc.flag |= VC_BCFOUT; break;
+ case 'S': vc.flag |= VC_VCFIN; break;
case 'c': vc.flag |= VC_CALL; break;
case 'v': vc.flag |= VC_VARONLY; break;
+ case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
case 't': vc.theta = atof(optarg); break;
case 'p': vc.pref = atof(optarg); break;
case 'P':
fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
fprintf(stderr, "Options: -c SNP calling\n");
fprintf(stderr, " -b output BCF instead of VCF\n");
+ fprintf(stderr, " -u uncompressed BCF output\n");
+ fprintf(stderr, " -S input is VCF\n");
fprintf(stderr, " -G suppress all individual genotype information\n");
fprintf(stderr, " -L discard the PL genotype field\n");
fprintf(stderr, " -v output potential variant sites only\n");
}
b = calloc(1, sizeof(bcf1_t));
- bp = bcf_open(argv[optind], "r");
- h = bcf_hdr_read(bp);
- if (vc.flag & VC_BCF) {
- bout = bcf_open("-", "w");
- bcf_hdr_write(bout, h);
- }
+ strcpy(moder, "r");
+ if (!(vc.flag & VC_VCFIN)) strcat(moder, "b");
+ strcpy(modew, "w");
+ if (vc.flag & VC_BCFOUT) strcat(modew, "b");
+ if (vc.flag & VC_UNCOMP) strcat(modew, "u");
+ bp = vcf_open(argv[optind], moder);
+ h = vcf_hdr_read(bp);
+ bout = vcf_open("-", modew);
+ vcf_hdr_write(bout, h);
if (vc.flag & VC_CALL) {
p1 = bcf_p1_init(h->n_smpl);
bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
}
if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
- if (optind + 1 < argc) {
+ if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
void *str2id = bcf_build_refhash(h);
if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
bcf_idx_t *idx;
}
}
}
- while (bcf_read(bp, h, b) > 0) {
+ while (vcf_read(bp, h, b) > 0) {
if (hash) {
uint64_t x = (uint64_t)b->tid<<32 | b->pos;
khint_t k = kh_get(set64, hash, x);
if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
update_bcf1(h->n_smpl, b, p1, &pr, vc.pref, vc.flag);
}
- if (vc.flag & VC_BCF) bcf_write(bout, h, b);
- else {
- char *vcf;
- if (vc.flag & VC_NO_GENO) {
- b->n_gi = 0;
- b->fmt[0] = '\0';
- }
- vcf = bcf_fmt(h, b);
- puts(vcf);
- free(vcf);
+ if (vc.flag & VC_NO_GENO) {
+ b->n_gi = 0;
+ b->fmt[0] = '\0';
}
+ vcf_write(bout, h, b);
++n_processed;
}
if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
bcf_hdr_destroy(h);
- bcf_close(bp); bcf_close(bout);
bcf_destroy(b);
+ vcf_close(bp); vcf_close(bout);
if (hash) kh_destroy(set64, hash);
if (vc.fn_list) free(vc.fn_list);
if (p1) bcf_p1_destroy(p1);
bgzf_open(const char* __restrict path, const char* __restrict mode)
{
BGZF* fp = NULL;
- if (mode[0] == 'r' || mode[0] == 'R') { /* The reading mode is preferred. */
+ if (strchr(mode, 'r') || strchr(mode, 'R')) { /* The reading mode is preferred. */
#ifdef _USE_KNETFILE
knetFile *file = knet_open(path, mode);
if (file == 0) return 0;
if (fd == -1) return 0;
fp = open_read(fd);
#endif
- } else if (mode[0] == 'w' || mode[0] == 'W') {
+ } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
int fd, oflag = O_WRONLY | O_CREAT | O_TRUNC;
#ifdef _WIN32
oflag |= O_BINARY;
#endif
fd = open(path, oflag, 0666);
if (fd == -1) return 0;
- fp = open_write(fd, strstr(mode, "u")? 1 : 0);
+ fp = open_write(fd, strchr(mode, 'u')? 1 : 0);
}
if (fp != NULL) fp->owned_file = 1;
return fp;
if (str) aux->p = str - 1, aux->tab[0] &= ~1ull;
else if (aux->tab[0]&1) return 0;
for (p = start = aux->p + 1; *p; ++p)
- if (aux->tab[*p/64]>>(*p%64)) break;
+ if (aux->tab[*p/64]>>(*p%64)&1) break;
aux->p = p; // end of token
if (*p == 0) aux->tab[0] |= 1; // no more tokens
return (char*)start;
projects / samtools.git / commitdiff