* convert BCF to QCALL input

diff --git a/bcftools/Makefile b/bcftools/Makefile
index 5a3dc763f8105ba3dc8db43db390a4b13c0ba252..95920256d2771459bbd56eebb018d44dfd9dc452 100644 (file)
--- a/bcftools/Makefile
+++ b/bcftools/Makefile
@@ -1,7 +1,7 @@
 CC=                    gcc
 CFLAGS=                -g -Wall -O2 #-m64 #-arch ppc
 DFLAGS=                -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
-LOBJS=         bcf.o vcf.o bcfutils.o prob1.o kfunc.o index.o fet.o
+LOBJS=         bcf.o vcf.o bcfutils.o prob1.o kfunc.o index.o fet.o bcf2qcall.o
 OMISC=         ..
 AOBJS=         call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o
 PROG=          bcftools

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;
+}

diff --git a/bcftools/call1.c b/bcftools/call1.c
index c0c24a6932c07bede41b8a3c0daba29dc82c07e7..08d759d453e92fc907e03431ccb3120a012f7ebf 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -23,6 +23,7 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define VC_HWE     128
 #define VC_KEEPALT 256
 #define VC_ACGT_ONLY 512
+#define VC_QCALL   1024
 
 typedef struct {
        int flag, prior_type, n1;
@@ -182,6 +183,7 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
 
 int bcfview(int argc, char *argv[])
 {
+       extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
        bcf_t *bp, *bout = 0;
        bcf1_t *b;
        int c;
@@ -196,7 +198,7 @@ int bcfview(int argc, char *argv[])
        tid = begin = end = -1;
        memset(&vc, 0, sizeof(viewconf_t));
        vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5;
-       while ((c = getopt(argc, argv, "N1:l:cHAGvLbSuP:t:p:")) >= 0) {
+       while ((c = getopt(argc, argv, "N1:l:cHAGvLbSuP:t:p:Q")) >= 0) {
                switch (c) {
                case '1': vc.n1 = atoi(optarg); break;
                case 'l': vc.fn_list = strdup(optarg); break;
@@ -212,6 +214,7 @@ int bcfview(int argc, char *argv[])
                case 'H': vc.flag |= VC_HWE; break;
                case 't': vc.theta = atof(optarg); break;
                case 'p': vc.pref = atof(optarg); break;
+               case 'Q': vc.flag |= VC_QCALL; break;
                case 'P':
                        if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
                        else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
@@ -233,6 +236,7 @@ int bcfview(int argc, char *argv[])
                fprintf(stderr, "         -H        perform Hardy-Weinberg test (slower)\n");
                fprintf(stderr, "         -v        output potential variant sites only\n");
                fprintf(stderr, "         -N        skip sites where REF is not A/C/G/T\n");
+               fprintf(stderr, "         -Q        output the QCALL likelihood format\n");
                fprintf(stderr, "         -1 INT    number of group-1 samples [0]\n");
                fprintf(stderr, "         -l FILE   list of sites to output [all sites]\n");
                fprintf(stderr, "         -t FLOAT  scaled mutation rate [%.4lg]\n", vc.theta);
@@ -251,7 +255,7 @@ int bcfview(int argc, char *argv[])
        bp = vcf_open(argv[optind], moder);
        h = vcf_hdr_read(bp);
        bout = vcf_open("-", modew);
-       vcf_hdr_write(bout, h);
+       if (!(vc.flag & VC_QCALL)) vcf_hdr_write(bout, h);
        if (vc.flag & VC_CALL) {
                p1 = bcf_p1_init(h->n_smpl);
                if (vc.prior_file) {
@@ -300,7 +304,11 @@ int bcfview(int argc, char *argv[])
                        if (!(l > begin && end > b->pos)) continue;
                }
                ++n_processed;
-               if (vc.flag & VC_CALL) {
+               if (vc.flag & VC_QCALL) { // output QCALL format; STOP here
+                       bcf_2qcall(h, b);
+                       continue;
+               }
+               if (vc.flag & VC_CALL) { // call variants
                        bcf_p1rst_t pr;
                        bcf_gl2pl(h->n_smpl, b);
                        bcf_p1_cal(b, p1, &pr); // pr.g[3] is not calculated here
@@ -312,7 +320,7 @@ int bcfview(int argc, char *argv[])
                        if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
                        update_bcf1(h->n_smpl, b, p1, &pr, vc.pref, vc.flag);
                }
-               if (vc.flag & VC_NO_GENO) {
+               if (vc.flag & VC_NO_GENO) { // do not output GENO fields
                        b->n_gi = 0;
                        b->fmt[0] = '\0';
                }