changes from git

[samtools.git] / bcftools / vcf.c

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index d8cb1e6d3efc56b8c119f677b25d292f696e3428..bc110847dab9e2b97d0248ddfef92312de561ce1 100644 (file)
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -124,10 +124,10 @@ int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
        if (!bp->is_vcf) return bcf_hdr_write(bp, h);
        if (h->l_txt > 0) {
                if (strstr(h->txt, "##fileformat=")) has_ver = 1;
-               if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
+               if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
                fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
        }
-       if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
+       if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
        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]);
@@ -182,9 +182,11 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
                                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) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+                                       } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
                                                ((uint8_t*)b->gi[i].data)[k-9] = 0;
-                                       } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+                                       } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+                                               ((int32_t*)b->gi[i].data)[k-9] = 0;
+                                       } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
                                                ((uint16_t*)b->gi[i].data)[k-9] = 0;
                                        } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
                                                int y = b->n_alleles * (b->n_alleles + 1) / 2;
@@ -199,12 +201,16 @@ 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) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+                               } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
                                        double _x = strtod(q, &q);
                                        int x = (int)(_x + .499);
                                        if (x > 255) x = 255;
                                        ((uint8_t*)b->gi[i].data)[k-9] = x;
-                               } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+                               } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+                                       int x = strtol(q, &q, 10);
+                                       if (x > 0xffff) x = 0xffff;
+                                       ((uint32_t*)b->gi[i].data)[k-9] = x;
+                               } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
                                        int x = strtol(q, &q, 10);
                                        if (x > 0xffff) x = 0xffff;
                                        ((uint16_t*)b->gi[i].data)[k-9] = x;