Imported Upstream version 0.1.10

[samtools.git] / bcftools / vcf.c

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index ebca869ed999faaed7e782f3a3c410badc062c1b..9b661ff5b4fbc29dde6a53b5e71c027f131a81f4 100644 (file)
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -156,7 +156,7 @@ 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)) {
+                                       } 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;
@@ -173,7 +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;