* change the order of PL/GL according to the latest VCF spec

[samtools.git] / bcftools / vcf.c

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index 6d3abaa495516014135e68f43225e7b97a7f5710..81a38eaa7f2d853908ce3df575416c9092735d76 100644 (file)
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -182,8 +182,10 @@ 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("SP", 2)) {
+                                               ((int32_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;
                                        } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
@@ -199,11 +201,15 @@ 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("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)) {
                                        int x = strtol(q, &q, 10);
                                        if (x > 0xffff) x = 0xffff;
@@ -224,7 +230,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
                                        y = b->n_alleles * (b->n_alleles + 1) / 2;
                                        for (j = 0; j < y; ++j) {
                                                x = strtod(q, &q);
-                                               data[(k-9) * y + j] = x;
+                                               data[(k-9) * y + j] = x > 0? -x/10. : x;
                                                ++q;
                                        }
                                }