Revert one of my earlier changes - Heng was right, CIGAR P not sensible in a padded...

[samtools.git] / bcftools / bcfutils.c

diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index 9608846bef3b435edf470d3b3ae8a075431e82b3..0eab4c1f322b398750fdda9da4caec6eea8e7579 100644 (file)
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -354,8 +354,6 @@ int bcf_gl10(const bcf1_t *b, uint8_t *gl)
        for (i = 0; i < b->n_smpl; ++i) {
                const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
                uint8_t *g = gl + 10 * i;
-               for (j = 0; j < PL->len; ++j)
-                       if (p[j]) break;
                for (k = j = 0; k < 4; ++k) {
                        for (l = k; l < 4; ++l) {
                                int t, x = map[k], y = map[l];
@@ -366,3 +364,27 @@ int bcf_gl10(const bcf1_t *b, uint8_t *gl)
        }
        return 0;
 }
+
+int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl)
+{
+       int k, l, j, i;
+       const bcf_ginfo_t *PL;
+       if (b->alt[0] == 0) return -1; // no alternate allele
+       for (i = 0; i < b->n_gi; ++i)
+               if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+       if (i == b->n_gi) return -1; // no PL
+       PL = b->gi + i;
+       for (i = 0; i < b->n_smpl; ++i) {
+               const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
+               uint8_t *g = gl + 10 * i;
+               for (k = j = 0; k < 4; ++k) {
+                       for (l = k; l < 4; ++l) {
+                               int t, x = k, y = l;
+                               if (x > y) t = x, x = y, y = t; // make sure x is the smaller
+                               x = y * (y+1) / 2 + x;
+                               g[j++] = x < PL->len? p[x] : 255;
+                       }
+               }
+       }
+       return 0;
+}