Imported Upstream version 0.1.9

[samtools.git] / bcftools / bcf2qcall.c

diff --git a/bcftools/bcf2qcall.c b/bcftools/bcf2qcall.c
new file mode 100644 (file)
index 0000000..8634c9e
--- /dev/null
+++ b/bcftools/bcf2qcall.c
@@ -0,0 +1,91 @@
+#include <errno.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
+#include "bcf.h"
+
+static int8_t nt4_table[256] = {
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4 /*'-'*/, 4, 4,
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  3, 4, 4, 4, -1, 4, 4, 4,  4, 4, 4, 4, 
+       4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  3, 4, 4, 4, -1, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
+};
+
+static int read_I16(bcf1_t *b, int anno[16])
+{
+       char *p;
+       int i;
+       if ((p = strstr(b->info, "I16=")) == 0) return -1;
+       p += 4;
+       for (i = 0; i < 16; ++i) {
+               anno[i] = strtol(p, &p, 10);
+               if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
+               ++p;
+       }
+       return 0;
+}
+
+int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b)
+{
+       int a[4], k, g[10], l, map[4], k1, j, i, i0, anno[16], dp, mq, d_rest;
+       char *s;
+       if (b->ref[1] != 0 || b->n_alleles > 4) return -1; // ref is not a single base
+       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
+       if (read_I16(b, anno) != 0) return -1; // no I16; FIXME: can be improved
+       d_rest = dp = anno[0] + anno[1] + anno[2] + anno[3];
+       if (dp == 0) return -1; // depth is zero
+       mq = (int)(sqrt((double)(anno[9] + anno[11]) / dp) + .499);
+       i0 = i;
+       a[0] = nt4_table[(int)b->ref[0]];
+       if (a[0] > 3) return -1; // ref is not A/C/G/T
+       a[1] = a[2] = a[3] = -2; // -1 has a special meaning
+       if (b->alt[0] == 0) return -1; // no alternate allele
+       map[0] = map[1] = map[2] = map[3] = -2;
+       map[a[0]] = 0;
+       for (k = 0, s = b->alt, k1 = -1; k < 3 && *s; ++k, s += 2) {
+               if (s[1] != ',' && s[1] != 0) return -1; // ALT is not single base
+               a[k+1] = nt4_table[(int)*s];
+               if (a[k+1] >= 0) map[a[k+1]] = k+1;
+               else k1 = k+1;
+               if (s[1] == 0) break;
+       }
+       for (k = 0; k < 4; ++k)
+               if (map[k] < 0) map[k] = k1;
+       for (i = 0; i < h->n_smpl; ++i) {
+               int d;
+               uint8_t *p = b->gi[i0].data + i * b->gi[i0].len;
+               for (j = 0; j < b->gi[i0].len; ++j)
+                       if (p[j]) break;
+               d = (int)((double)d_rest / (h->n_smpl - i) + .499);
+               if (d == 0) d = 1;
+               if (j == b->gi[i0].len) d = 0;
+               d_rest -= d;
+               for (k = j = 0; k < 4; ++k) {
+                       for (l = k; l < 4; ++l) {
+                               int t, x = map[k], y = map[l];
+                               if (x > y) t = x, x = y, y = t;
+                               g[j++] = p[x * b->n_alleles - x * (x-1) / 2 + (y - x)];
+                       }
+               }
+               printf("%s\t%d\t%c", h->ns[b->tid], b->pos+1, *b->ref);
+               printf("\t%d\t%d\t0", d, mq);
+               for (j = 0; j < 10; ++j)
+                       printf("\t%d", g[j]);
+               printf("\t%s\n", h->sns[i]);
+       }
+       return 0;
+}