int main(int argc, char **argv)
{
if ( argc!=2 )
{
fprintf(stderr,"Usage: test-vcf-sweep <file.bcf|file.vcf>\n");
return 1;
}
// Init variables. The checksum is just for this test program to output
// something and verify that all sites are read in both passes - fwd and
// bwd.
bcf_sweep_t *sw = bcf_sweep_init(argv[1]);
bcf_hdr_t *hdr = bcf_sweep_hdr(sw);
int chksum = 0;
// First we must sweep forward and read the whole file to build an index.
// If this is undesirable, we can require the presence of a .gzi index
// which can be created with `bgzip -r` from the samtools/htslib package
bcf1_t *rec;
while ( (rec = bcf_sweep_fwd(sw)) ) chksum += rec->pos+1;
printf("fwd position chksum: %d\n", chksum);
// Now sweep backward.
chksum = 0;
while ( (rec = bcf_sweep_bwd(sw)) ) chksum += rec->pos+1;
printf("bwd position chksum: %d\n", chksum);
// And forward and backward again, this time summing the PL vectors
int i,j, mPLs = 0, nPLs;
int32_t *PLs = NULL;
chksum = 0;
while ( (rec = bcf_sweep_fwd(sw)) )
{
// get copy of the PL vectors
nPLs = bcf_get_format_int32(hdr, rec, "PL", &PLs, &mPLs);
if ( !nPLs ) continue; // PL not present
// how many values are there per sample
int nvals = nPLs / bcf_hdr_nsamples(hdr);
int32_t *ptr = PLs;
for (i=0; i<bcf_hdr_nsamples(hdr); i++)
{
for (j=0; j<nvals; j++)
{
// check for shorter vectors (haploid genotypes amongst diploids)
if ( ptr[j]==bcf_int32_vector_end ) break;
// skip missing values
if ( ptr[j]==bcf_int32_missing ) continue;
chksum += ptr[j];
}
ptr += nvals;
}
}
printf("fwd PL chksum: %d\n", chksum);
// And the same backwards..
chksum = 0;
while ( (rec = bcf_sweep_bwd(sw)) )
{
nPLs = bcf_get_format_int32(hdr, rec, "PL", &PLs, &mPLs);
if ( !nPLs ) continue;
int nvals = nPLs / bcf_hdr_nsamples(hdr);
int32_t *ptr = PLs;
for (i=0; i<bcf_hdr_nsamples(hdr); i++)
{
for (j=0; j<nvals; j++)
{
if ( ptr[j]==bcf_int32_vector_end ) break;
if ( ptr[j]==bcf_int32_missing ) continue;
chksum += ptr[j];
}
ptr += nvals;
}
}
printf("bwd PL chksum: %d\n", chksum);
// Clean up
bcf_sweep_destroy(sw);
return 0;
}
/**************************
* PROCESS INPUT VCF FILE *
**************************/
void vcf2raw(char **filename, char **out_filename, char **cross, int *n_parent1,
char **parent1, int *n_parent2, char **parent2, double *min_class) {
// We assume the input file exists (checked in R)
bcf_sweep_t *in_vcf = bcf_sweep_init(*filename);
if (in_vcf == NULL) {
bcf_sweep_destroy(in_vcf);
error("Could not parse input VCF file.");
}
bcf_hdr_t *vcf_hdr = bcf_sweep_hdr(in_vcf);
// Get reference sequence IDs
int n_seq = 0;
const char **seq_names = NULL;
seq_names = bcf_hdr_seqnames(vcf_hdr, &n_seq);
if (seq_names == NULL || n_seq == 0) {
free(seq_names);
error("Could not correctly parse sequence names in VCF file. Is the input file tabix indexed?\n");
}
// Map parent names to sample indices
int idx_parent1[*n_parent1];
int idx_parent2[*n_parent2];
get_parents_idx(*n_parent1, idx_parent1, *n_parent2, idx_parent2, vcf_hdr, parent1, parent2);
// Get progeny sample indices (all samples that are not set as parents)
int n_samples = bcf_hdr_nsamples(vcf_hdr);
int n_progeny = n_samples - *n_parent1 - *n_parent2;
if (n_progeny == 0) {
error("Input file must contain at least one progeny individual.");
}
int idx_progeny[n_progeny];
int i = 0, s;
for (s = 0; s < n_samples; s++) {
if (!is_val_in_arr(s, idx_parent1, *n_parent1)) {
if (!is_val_in_arr(s, idx_parent2, *n_parent2)) {
idx_progeny[i++] = s;
}
}
}
// Minimum count to assign parent genotype
int min_class_parent1 = (int)ceil(*min_class * *n_parent1);
int min_class_parent2 = (int)ceil(*min_class * *n_parent2);
// Convert cross type
int cross_type = get_cross_type(cross);
// We need to write to a temporary file, because the number of markers in the header is unknown
FILE *temp_f;
char temp_filename[] = "tmp_raw_XXXXXX";
int temp_fd;
temp_fd = mkstemp(temp_filename);
if (temp_fd == -1) {
error("Could not open temporary output file.\n");
}
unlink(temp_filename);
temp_f = fdopen(temp_fd, "w+");
if (temp_f == NULL) {
error("Could not open temporary output file.\n");
}
// CHROM and POS fields will be placed at the end of the output file
int marker_count = 0;
int * chrom = malloc(MAX_VARIANTS * sizeof(int));
if (chrom == NULL) {
error("Could not allocate vector.\n");
}
int * pos = malloc(MAX_VARIANTS * sizeof(int));
if (pos == NULL) {
error("Could not allocate vector.\n");
}
// Mapping of VCF genotypes to ONEMAP genotypes
const char * const D_BC_ref[GT_TYPES_LEN] = { "a", "-", "ab", "-", "-", "-", "-" };
const char * const D_BC_alt[GT_TYPES_LEN] = { "-", "a", "ab", "-", "-", "-", "-" };
const char * const RI_ref[GT_TYPES_LEN] = { "a", "b", "-", "-", "-", "-", "-" };
const char * const RI_alt[GT_TYPES_LEN] = { "b", "a", "-", "-", "-", "-", "-" };
const char * const B3_F2_ref[GT_TYPES_LEN] = { "a", "b", "ab", "-", "-", "-", "-" };
const char * const B3_F2_alt[GT_TYPES_LEN] = { "b", "a", "ab", "-", "-", "-", "-" };
// Scan all records in VCF file and print valid markers to output
bcf1_t *record;
int32_t *GTs = NULL;
int nGT_arr = 0;
while ((record = bcf_sweep_fwd(in_vcf)) && marker_count < MAX_VARIANTS) {
// We only consider biallelic SNP and INDEL markers
int var_type = bcf_get_variant_types(record);
if ((var_type == VCF_SNP || var_type == VCF_INDEL) && record->n_allele == 2) {
int nGTs = bcf_get_format_int32(vcf_hdr, record, "GT", >s, &nGT_arr);
// We only consider diploid variants (number of alleles in genotypes == 2)
nGTs /= n_samples;
if (nGTs == 2) {
bcf_fmt_t *fmt_ptr = bcf_get_fmt(vcf_hdr, record, "GT");
// First, check which parents are heterozygous or homozygous (REF or ALT allele)
bool is_het_parent1 = false, is_hom_ref_parent1 = false, is_hom_alt_parent1 = false;
get_consensus_parent_gt(fmt_ptr, *n_parent1, idx_parent1, min_class_parent1, &is_het_parent1,
&is_hom_ref_parent1, &is_hom_alt_parent1);
bool is_het_parent2 = false, is_hom_ref_parent2 = false, is_hom_alt_parent2 = false;
get_consensus_parent_gt(fmt_ptr, *n_parent2, idx_parent2, min_class_parent2, &is_het_parent2,
&is_hom_ref_parent2, &is_hom_alt_parent2);
// Convert to appropriate marker type
char marker_type[MARKER_TYPE_LEN];
int type = get_marker_type(marker_type, cross_type,
is_het_parent1, is_hom_ref_parent1, is_hom_alt_parent1,
is_het_parent2, is_hom_ref_parent2, is_hom_alt_parent2);
const char * const(*type_ptr)[GT_TYPES_LEN];
bool valid_marker = true;
switch(type)
{
case marker_B3:
case marker_F2_ref:
type_ptr = &B3_F2_ref;
break;
case marker_F2_alt:
type_ptr = &B3_F2_alt;
break;
case marker_D_ref:
case marker_BC_ref:
type_ptr = &D_BC_ref;
break;
case marker_D_alt:
case marker_BC_alt:
type_ptr = &D_BC_alt;
break;
case marker_RI_ref:
type_ptr = &RI_ref;
break;
case marker_RI_alt:
type_ptr = &RI_alt;
break;
default:
valid_marker = false;
}
if (valid_marker) {
// Store CHROM and POS fields for valid markers
chrom[marker_count] = record->rid;
pos[marker_count] = record->pos + 1;
// Check if marker name exists; if negative, create one
char *marker_name = record->d.id;
if (!strcmp(marker_name, ".")) {
sprintf(marker_name, "%s.%d", seq_names[chrom[marker_count]], pos[marker_count]);
}
// Output variant in ONEMAP format to temporary file
print_record(temp_f, marker_name, marker_type, fmt_ptr, n_progeny, idx_progeny, type_ptr);
marker_count++;
}
}
}
}
// Write final output file header
FILE *final_f = fopen(*out_filename, "w");
if (final_f == NULL) {
error("Could not open output file.\n");
}
fprintf(final_f, "data type %s\n", *cross);
// The next header line contains the following information: number of individuals, number of markers, 1 for the presence of CHROM information, 1 for the presence of POS information and 0 for the absence of phenotypes (these need to be manually included later)
fprintf(final_f, "%d %d 1 1 0\n", n_progeny, marker_count);
// The next header line contains the sample names
char *cur_sample_name = vcf_hdr->samples[idx_progeny[0]];
fprintf(final_f, "%s", cur_sample_name);
for (i = 1; i < n_progeny; i++) {
cur_sample_name = vcf_hdr->samples[idx_progeny[i]];
fprintf(final_f, "\t%s", cur_sample_name);
}
fprintf(final_f, "\n");
// Copy marker data from temporary file to final file
rewind(temp_f);
char buf[BUFSIZ];
size_t size;
while ((size = fread(buf, 1, BUFSIZ, temp_f))) {
fwrite(buf, 1, size, final_f);
}
// Write CHROM and POS data to output file
if (marker_count) {
fprintf(final_f, "*CHROM\t");
fprintf(final_f, "%s", seq_names[chrom[0]]);
for (i = 1; i < marker_count; i++) {
fprintf(final_f, " %s", seq_names[chrom[i]]);
}
fprintf(final_f, "\n*POS\t");
fprintf(final_f, "%d", pos[0]);
for (i = 1; i < marker_count; i++) {
fprintf(final_f, " %d", pos[i]);
}
}
// Clean-up
free(chrom);
free(pos);
free(GTs);
bcf_sweep_destroy(in_vcf);
fclose(temp_f);
close(temp_fd);
fclose(final_f);
}