* samtools-0.1.9-1 (r786)

[samtools.git] / bcftools / vcf.c

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index 23aad3c0c97b02c12d9643d18c87e68ef4d87dc2..9b661ff5b4fbc29dde6a53b5e71c027f131a81f4 100644 (file)
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -102,13 +102,6 @@ int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
                if (strstr(h->txt, "##SQ=")) has_ref = 1;
        }
        if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
-       if (!has_ref) {
-               fprintf(v->fpout, "##SQ=");
-               for (i = 0; i < h->n_ref; ++i) {
-                       fprintf(v->fpout, "%s", h->ns[i]);
-                       fputc(i == h->n_ref - 1? '\n' : ',', 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]);
@@ -139,6 +132,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
        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;
+       b->n_smpl = h->n_smpl;
        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
@@ -152,17 +146,17 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
                } else if (k == 1) { // pos
                        b->pos = atoi(p) - 1;
                } else if (k == 5) { // qual
-                       b->qual = (p[0] >= '0' && p[0] <= '9')? atoi(p) : 0;
+                       b->qual = (p[0] >= '0' && p[0] <= '9')? atof(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);
+                       if (k == 8) bcf_sync(b);
                } else { // k > 9
                        if (strncmp(p, "./.", 3) == 0) {
                                for (i = 0; i < b->n_gi; ++i) {
                                        if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
                                                ((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
-                                       } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
+                                       } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
                                                ((uint8_t*)b->gi[i].data)[k-9] = 0;
                                        } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
                                                ((uint16_t*)b->gi[i].data)[k-9] = 0;
@@ -179,7 +173,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
                        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)) {
+                               } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
                                        double _x = strtod(q, &q);
                                        int x = (int)(_x + .499);
                                        if (x > 255) x = 255;