support trio indels

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index aeae6ca0de411f198f4ff76d7c29f99a19f54448..822ae5cf80fd7f9dc375259524935c933f088323 100644 (file)
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.h
@@ -28,7 +28,7 @@
 #ifndef BCF_H
 #define BCF_H
 
-#define BCF_VERSION "0.1.17 (r973:277)"
+#define BCF_VERSION "0.1.17-dev (r973:277)"
 
 #include <stdint.h>
 #include <zlib.h>
@@ -154,6 +154,8 @@ extern "C" {
        int bcf_fix_pl(bcf1_t *b);
        // convert PL to GLF-like 10-likelihood GL
        int bcf_gl10(const bcf1_t *b, uint8_t *gl);
+       // convert up to 4 INDEL alleles to GLF-like 10-likelihood GL
+       int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl);
 
        // string hash table
        void *bcf_build_refhash(bcf_hdr_t *h);

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;
+}

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 69bd5f7700698dfe39207695328220a4d8eba248..b0baee2ea1b346e24eadd2d9bccea0ed6e886f6a 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -495,7 +495,7 @@ int bcfview(int argc, char *argv[])
                        if (!(l > begin && end > b->pos)) continue;
                }
                ++n_processed;
-               if (vc.flag & VC_QCNT) { // summarize the difference
+               if ((vc.flag & VC_QCNT) && !is_indel) { // summarize the difference
                        int x = bcf_min_diff(b);
                        if (x > 255) x = 255;
                        if (x >= 0) ++qcnt[x];

diff --git a/bcftools/mut.c b/bcftools/mut.c
index 4b7cd104a60b7bc3d4fba7086b551ac72155f350..15ef265b25b38ce3b3894eebdd52e6496cb0135b 100644 (file)
--- a/bcftools/mut.c
+++ b/bcftools/mut.c
@@ -33,6 +33,7 @@ uint32_t *bcf_trio_prep(int is_x, int is_son)
        return ret;
 }
 
+
 int bcf_trio_call(const uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt)
 {
        int i, j, k;
@@ -44,7 +45,9 @@ int bcf_trio_call(const uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt)
                if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
        if (i == b->n_gi) return -1; // no PL
        gl10 = alloca(10 * b->n_smpl);
-       if (bcf_gl10(b, gl10) < 0) return -1;
+       if (bcf_gl10(b, gl10) < 0) {
+               if (bcf_gl10_indel(b, gl10) < 0) return -1;
+       }
        PL = b->gi + i;
        for (i = 0, k = 0; i < 4; ++i)
                for (j = i; j < 4; ++j)

diff --git a/ksort.h b/ksort.h
index b8b62f189c557a8aa77fbdfbb93e7dafb3acba14..fa850ab0762a9225bae5b3bcad6739a3bb6a3c27 100644 (file)
--- a/ksort.h
+++ b/ksort.h
@@ -60,10 +60,6 @@
 #include <stdlib.h>
 #include <string.h>
 
-#ifdef _WIN32
-#define drand48() ((double)rand() / RAND_MAX)
-#endif
-
 typedef struct {
        void *left, *right;
        int depth;