static void report_qual_type(char min_qual, char max_qual) {
fprintf(stderr, "\n");
fprintf(stderr, "guessing quality format:\n");
if((min_qual == -1) || (max_qual == -1)) {
fprintf(stderr, " no valid quality scores to guess quality type from\n");
}
fprintf(stderr, " min_qual:%c, max_qual:%c\n", min_qual, max_qual);
if(min_qual < MIN_QUAL_SOLEXA) {
fprintf(stderr, " quality vals appear to be Sanger / Illum 1.8+ format"
" (Phred+33)\n");
if(max_qual >= 'h') {
my_warn("%s:%d: quality vals may be mix of Phred+33 and Phred+64\n"
" You should probably fix this.", __FILE__, __LINE__);
}
} else {
if(min_qual < MIN_QUAL_ILLUM_1_3) {
my_warn("%s:%d: quality vals appear to be OLD solexa format, "
"may need to convert prior to processing.\n", __FILE__, __LINE__);
}
else if(min_qual < MIN_QUAL_ILLUM_1_5) {
fprintf(stderr, " quality vals appear to be Illumina 1.3+ format "
"(Phred+64)\n should probably use -I flag for bwa aln "
"(relevant only if using -q argument)\n");
}
else {
fprintf(stderr, " quality vals appear to be Illumina 1.5+ format "
"(Phred+64)\n should probably use -I flag for bwa aln "
"(relevant only if using -q argument)\n");
}
}
}
/**
* sets attributes of the provided SeedMatch data structure to give
* the total number of matches and kmer id(s) for the provided
* nucleotide array. The kmer ids can be used to index matches in
* the seed match table. There can be multiple kmer ids, because the
* nucleotides are allowed to contain ambiguity codes.
*/
void seed_table_lookup(SeedTable *seed_tab, unsigned char *nucs,
SeedMatch *seed_match) {
unsigned int kmer_id, i;
unsigned char **unambig;
if(ambi_has_ambi(nucs, seed_tab->seed_len)) {
/* this seed contains ambiguous nucleotides. convert
* to all possible seeds containing non-ambiguous nucleotides.
*/
seed_match->n_kmer = ambi_resolve(nucs, seed_tab->seed_len,
seed_tab->unambig_nucs,
SEED_TABLE_MAX_UNAMBIG);
if(seed_match->n_kmer == 0) {
my_warn("seed contains too many ambiguous nucleotides");
}
unambig = seed_tab->unambig_nucs;
/* count total number of matches, set kmer ids */
seed_match->n_match = 0;
for(i = 0; i < seed_match->n_kmer; i++) {
kmer_id = kmer_nucs_to_id(unambig[i], seed_tab->seed_len);
seed_match->n_match += seed_tab->n_match[kmer_id];
seed_match->kmer_ids[i] = kmer_id;
}
} else {
/* there were no ambiguous nucleotides, just use original seed */
kmer_id = kmer_nucs_to_id(nucs, seed_tab->seed_len);
seed_match->n_match = seed_tab->n_match[kmer_id];
seed_match->n_kmer = 1;
seed_match->kmer_ids[0] = kmer_id;
}
}
char *my_read(int fd, int ret)
{
static int i = 0;
static char buff[4097];
if (i == 0 || buff[i] == '\0')
{
i = 0;
if ((ret = read(fd, buff, 4096)) > 0 && !my_str_isprintable(buff))
ret = my_fread(buff, fd);
if (ret <= 0)
{
if (ret)
my_warn(NULL, fd);
return (NULL);
}
buff[ret] = '\0';
}
ret = i;
while (buff[i] && buff[i] != '\n' && buff[i] != ';')
jump_inhibitors(buff, &i);
if (buff[i])
i = i + 1;
return (read_one_line(buff + ret));
}
static int check_seq(ReadSeq *read) {
int i, j;
char c;
int err;
/* string of valid nucleotide identifiers, including ambiguity codes */
static const char *valid_nucs = "ATCGNatcgnMRWSYKmrwsyk";
err = FALSE;
for(i = 0; i < read->read_len; i++) {
c = read->line2[i];
j = 0;
while(c != valid_nucs[j]) {
if(valid_nucs[j] == '\0') {
my_warn("%s:%d: read contains invalid base '%c'",
__FILE__, __LINE__, c);
err = TRUE;
break;
}
j++;
}
if(err) {
read->status = FASTQ_ERR;
break;
}
}
return read->status;
}
/**
* Checks that the header has expected 7 fields. This could be changed
* to allow for variety of header types.
*/
static int check_header(ReadSeq *read) {
char *offset;
size_t assigned;
/* parse read attributes from header line, assuming it has standard
* formatting. Example header line:
* IPAR1:1:2:18330:12837#0/1
*/
offset = index(read->line1, ':');
if(offset == NULL) {
assigned = 0;
} else {
/* replace first ':' with ' ', so that string directive of
* sscanf stops after parsing machine name
*/
offset[0] = ' ';
/* parse attributes */
assigned = sscanf(read->line1, "@%s %d:%d:%d:%d#%d/%d",
read->machine, &read->lane, &read->tile, &read->x,
&read->y, &read->run_num, &read->type);
offset[0] = ':';
}
if(assigned != 7) {
/* failed to completely parse header */
my_warn("%s:%d: could only parse %d out of 7 expected fields from header",
__FILE__, __LINE__, assigned);
read->status = FASTQ_ERR;
}
return read->status;
}
/**
* Parses a read in fastq format.
* Returns FASTQ_END at end of file, FASTQ_OK on success, FASTQ_ERR on problem
*/
static int parse_fastq_read(ReadSeq *read, gzFile f) {
size_t qual_len;
read->status = FASTQ_OK;
read_fastq_lines(read, f);
if(read->status != FASTQ_OK) {
return read->status;
}
/* check_header(read); */
/* if(read->status != FASTQ_OK) { */
/* return read->status; */
/* } */
/* third line should start with '+' separator */
if(read->line3[0] != '+') {
my_warn("%s:%d: third line does not start with '+'",
__FILE__, __LINE__);
read->status = FASTQ_ERR;
return read->status;
}
/* check length of read and quality */
read->read_len = strlen(read->line2);
qual_len = strlen(read->line4);
if(read->read_len < 1) {
my_warn("%s:%d: read has no bases\n", __FILE__, __LINE__);
return read->status;
}
/* next line should be quality scores */
if(read->read_len != qual_len) {
my_warn("%s:%d: read len (%ld) does not match quality score len (%ld)",
__FILE__, __LINE__, read->read_len, qual_len);
read->status = FASTQ_ERR;
return read->status;
}
check_seq(read);
check_qual(read);
return read->status;
}
void vcf_read_header(gzFile vcf_fh, VCFInfo *vcf_info) {
char *line, *cur, *token;
int tok_num;
int n_fix_header, i;
/* const char delim[] = " \t"; */
const char delim[] = "\t";
n_fix_header = sizeof(vcf_fix_headers) / sizeof(const char *);
vcf_info->n_header_line = 0;
while(util_gzgetline(vcf_fh, &vcf_info->buf, &vcf_info->buf_size) != -1) {
line = vcf_info->buf;
if(util_str_starts_with(line, "##")) {
/* header line */
vcf_info->n_header_line += 1;
}
else if(util_str_starts_with(line, "#CHROM")) {
/* this should be last header line that contains list of fixed fields */
vcf_info->n_header_line += 1;
cur = vcf_info->buf;
line = util_str_dup(vcf_info->buf);
tok_num = 0;
while((token = strsep(&cur, delim)) != NULL) {
if(tok_num < n_fix_header) {
if(strcmp(token, vcf_fix_headers[tok_num]) != 0) {
my_warn("expected token %d to be %s but got '%s'",
tok_num, vcf_fix_headers[tok_num], token);
}
}
tok_num += 1;
}
vcf_info->n_sample = tok_num - n_fix_header;
/*
* read sample names from remaining part of header
*/
vcf_info->sample_names = my_malloc(sizeof(char *) * vcf_info->n_sample);
cur = line;
tok_num = 0;
i = 0;
while((token = strsep(&cur, delim)) != NULL) {
if(tok_num >= n_fix_header) {
vcf_info->sample_names[i] = util_str_dup(token);
i += 1;
}
tok_num += 1;
}
my_free(line);
break;
} else {
my_err("expected last line in header to start with #CHROM");
}
}
}
/**
* Checks that quality characters fall within valid range
*/
static int check_qual(ReadSeq *read) {
int i;
char c;
read->min_qual = -1;
read->max_qual = -1;
for(i = 0; i < read->read_len; i++) {
c = read->line4[i];
if(read->min_qual == -1) {
read->min_qual = c;
read->max_qual = c;
} else {
if(c < read->min_qual) {
read->min_qual = c;
}
if(c > read->max_qual) {
read->max_qual = c;
}
}
}
if(read->min_qual < MIN_QUAL) {
my_warn("%s:%d: read has invalid quality value with ascii code %d",
__FILE__, __LINE__, read->min_qual);
read->status = FASTQ_ERR;
}
if(read->max_qual > MAX_QUAL) {
my_warn("%s:%d: read has invalid quality value with ascii code %d",
__FILE__, __LINE__, read->max_qual);
read->status = FASTQ_ERR;
}
return read->status;
}
/**
* Adds location for a seed match to the provided seed table.
*/
void seed_table_add_match(SeedTable *seed_tab, unsigned int offset,
unsigned char *nucs) {
unsigned int kmer_id, i, j;
int n_unambig;
unsigned char **unambig;
if(seed_tab->match_buf == NULL) {
seed_tab_init_match_mem(seed_tab);
}
/* convert seeds with ambiguity codes to all possible
* non-ambiguous seqs
*/
if(ambi_has_ambi(nucs, seed_tab->seed_len)) {
n_unambig = ambi_resolve(nucs, seed_tab->seed_len,
seed_tab->unambig_nucs,
SEED_TABLE_MAX_UNAMBIG);
if(n_unambig == 0) {
my_warn("seed contains too many ambiguous nucleotides");
return;
}
unambig = seed_tab->unambig_nucs;
} else {
/* no ambiguous nucleotides, just use original seed */
unambig = &nucs;
n_unambig = 1;
}
for(i = 0; i < n_unambig; i++) {
kmer_id = kmer_nucs_to_id(unambig[i], seed_tab->seed_len);
/* cur is number of matches already added to array */
j = seed_tab->cur[kmer_id];
if(j >= seed_tab->n_match[kmer_id]) {
my_err("%s:%d: more matches than expected to kmer",
__FILE__, __LINE__);
}
/* add genomic position (offset) to match array */
seed_tab->match[kmer_id][j] = offset;
/* update cur to point to next element of match array */
seed_tab->cur[kmer_id] += 1;
}
}
static void check_line_len(ReadSeq *read, char *line, gzFile f) {
size_t len, n;
char c;
len = strlen(line);
if(len == 0) {
return;
}
if(line[len-1] == '\n') {
return;
}
/* line did not terminate with a '\n' */
my_warn("%s:%d: line did not terminate with '\\n': \n'%s'\n",
__FILE__, __LINE__, line, len);
read->status = FASTQ_ERR;
/* seek in file until next '\n' is found */
n = 0;
while((c = gzgetc(f)) != -1) {
n++;
if(n < 10) {
if(isprint(c)) {
fprintf(stderr, " extra character %ld: '%c'\n", n, c);
}
else {
fprintf(stderr, " unprintable extra character %ld: '\\%d'\n", n, c);
}
} else if(n == 10) {
fprintf(stderr, " ...\n");
}
if(c == '\n') {
fprintf(stderr, " read %ld extra characters to reach end of line\n", n);
return;
}
}
fprintf(stderr, " read %ld extra characters to reach end of file\n", n);
return;
}
/**
* Counts a seed match, but does not actually add its location
* to the seed table
*/
void seed_table_count_match(SeedTable *seed_tab, unsigned char *nucs) {
unsigned int kmer_id;
unsigned char **unambig;
int n_unambig, i;
/* convert seeds with ambiguity codes to all possible
* non-ambiguous seqs
*/
if(ambi_has_ambi(nucs, seed_tab->seed_len)) {
n_unambig = ambi_resolve(nucs, seed_tab->seed_len,
seed_tab->unambig_nucs,
SEED_TABLE_MAX_UNAMBIG);
if(n_unambig == 0) {
my_warn("seed contains too many ambiguous nucleotides");
return;
}
unambig = seed_tab->unambig_nucs;
} else {
/* no ambiguous nucleotides, just use original seed */
unambig = &nucs;
n_unambig = 1;
}
for(i = 0; i < n_unambig; i++) {
kmer_id = kmer_nucs_to_id(unambig[i], seed_tab->seed_len);
/* increment number of matches to this kmer */
if(seed_tab->n_match[kmer_id] == UINT_MAX) {
my_err("%s:%d maximum number of seed matches (%u) "
"exceeded for kmer %u", __FILE__, __LINE__,
UINT_MAX, kmer_id);
}
seed_tab->n_match[kmer_id] += 1;
seed_tab->total_match += 1;
}
}
void map_reads(gzFile *output_files, gzFile multi_out_file,
gzFile unmapped_out_file, gzFile reads_f, Mapper *mapper,
int reads_format, int output_type) {
FastqRead fastq_read;
MapRead map_read;
long warn_count, n_fastq_rec, n_fastq_err;
long n_map_uniq, n_map_multi, n_map_none;
map_read.fwd_nucs = my_new(unsigned char, FASTQ_MAX_LINE);
map_read.rev_nucs = my_new(unsigned char, FASTQ_MAX_LINE);
n_map_uniq = n_map_multi = n_map_none = 0;
warn_count = n_fastq_err = n_fastq_rec = 0;
/* loop over all records in FASTQ file */
while(TRUE) {
long r = 0;
/* read fastq record from file */
if(reads_format == READS_FORMAT_FASTQ) {
r = fastq_parse_read(&fastq_read, reads_f);
}
else if(reads_format == READS_FORMAT_QSEQ) {
r = fastq_parse_qseq_read(&fastq_read, reads_f);
}
else {
my_err("%s:%d: unknown read format", __FILE__, __LINE__);
}
if(r == FASTQ_END) {
/* we have reached the end of the file */
break;
}
if(r == FASTQ_ERR) {
/* this fastq record contains an error */
if(warn_count < FASTQ_MAX_WARN) {
warn_count += 1;
my_warn("%s:%d: skipping invalid fastq record:\n",
__FILE__, __LINE__);
fprintf(stderr, " %s\n %s\n %s\n %s\n", fastq_read.line1,
fastq_read.line2, fastq_read.line3, fastq_read.line4);
}
n_fastq_err += 1;
}
else if(fastq_read.read_len != mapper->seed_finder_fwd->read_len) {
/* check that read length is correct */
warn_count += 1;
my_warn("%s:%d: specified read length is %u, but got %d, "
"skipping read\n", __FILE__, __LINE__,
mapper->seed_finder_fwd->read_len, fastq_read.read_len);
n_fastq_err += 1;
}
else if(r == FASTQ_OK) {
n_fastq_rec += 1;
read_from_fastq_record(&map_read, &fastq_read);
if((n_fastq_rec % 1000000) == 0) {
fprintf(stderr, ".");
}
/* try to map this read to genome */
mapper_map_one_read(mapper, &map_read);
if(map_read.map_code == MAP_CODE_NONE) {
/* read does not map to genome */
n_map_none += 1;
if(output_type == OUTPUT_TYPE_SINGLE) {
write_unmapped_read(output_files[0], &map_read);
} else {
write_unmapped_read(unmapped_out_file, &map_read);
}
}
else if(map_read.map_code == MAP_CODE_MULTI) {
/* read maps to multiple genomic locations */
n_map_multi += 1;
if(output_type == OUTPUT_TYPE_SINGLE) {
write_read(output_files, mapper->chr_tab, &map_read, FALSE);
} else {
write_read(&multi_out_file, mapper->chr_tab, &map_read, FALSE);
}
}
else if(map_read.map_code == MAP_CODE_UNIQUE) {
/* read maps to single genomic location */
n_map_uniq += 1;
if(output_type == OUTPUT_TYPE_SINGLE) {
write_read(output_files, mapper->chr_tab, &map_read, FALSE);
} else {
write_read(output_files, mapper->chr_tab, &map_read, TRUE);
}
}
else {
my_err("%s:%d: unknown mapping code", __FILE__, __LINE__);
}
} else {
my_err("%s:%d: unknown fastq status", __FILE__, __LINE__);
}
}
fprintf(stderr, "\ndone\n");
fprintf(stderr, "fastq errors: %ld\n", n_fastq_err);
fprintf(stderr, "fastq records (without errors): %ld\n", n_fastq_rec);
fprintf(stderr, "unmapped reads: %ld\n", n_map_none);
fprintf(stderr, "uniquely mapping reads: %ld\n", n_map_uniq);
fprintf(stderr, "multiply mapping reads: %ld\n", n_map_multi);
my_free(map_read.fwd_nucs);
my_free(map_read.rev_nucs);
}
void merge_vcf(int n_vcf, char **vcf_filenames) {
FileInfo *f_info;
int n_done, n_chrom, i, *is_lowest, *lowest, n_lowest;
int ret, use_geno_probs, use_haplotypes;
Chromosome *chrom_tab;
f_info = init_file_info(n_vcf, vcf_filenames);
/* find chromosomes that are present in ALL VCFs */
chrom_tab = chrom_table_intersect(f_info, n_vcf, &n_chrom);
n_done = 0;
is_lowest = my_malloc(sizeof(int) * n_vcf);
lowest = my_malloc(sizeof(int) * n_vcf);
/* only use genotypes and haplotypes if they are present in ALL files */
use_geno_probs = TRUE;
use_haplotypes = TRUE;
/* read first SNP from all files */
for(i = 0; i < n_vcf; i++) {
ret = vcf_read_line(f_info[i].gzf, f_info[i].vcf, &f_info[i].cur_snp);
if(ret == -1) {
/* file is over */
n_done += 1;
f_info[i].is_done = TRUE;
my_warn("file %s contains no SNPs\n", vcf_filenames[i]);
f_info[i].cur_chrom = NULL;
} else {
set_cur_chrom(&f_info[i], chrom_tab, n_chrom);
if(!f_info[i].cur_snp.has_geno_probs) {
if(use_geno_probs) {
fprintf(stderr, "Not using genotype likelihoods (GL) because "
"not present in file %s\n", vcf_filenames[i]);
}
use_geno_probs = FALSE;
}
if(!f_info[i].cur_snp.has_haplotypes) {
if(use_haplotypes) {
fprintf(stderr, "Not using genotypes (GT) because "
"not present in file %s\n", vcf_filenames[i]);
}
use_haplotypes = FALSE;
}
}
}
fprintf(stderr, "parsing files\n");
while(n_done < n_vcf) {
/* find SNP(s) with lowest (chrom, pos) */
find_lowest(f_info, n_vcf, is_lowest, lowest, &n_lowest);
/* merge counts and write line for these SNPs */
write_output(stdout, f_info, n_vcf, is_lowest, lowest,
use_geno_probs, use_haplotypes);
/* advance files with lowest SNPs */
for(i = 0; i < n_vcf; i++) {
if(!f_info[i].is_done && is_lowest[i]) {
if(vcf_read_line(f_info[i].gzf, f_info[i].vcf, &f_info[i].cur_snp) == -1) {
/* have reached end of this file */
n_done += 1;
f_info[i].is_done = TRUE;
}
}
}
}
fprintf(stderr, "done!\n");
free_file_info(f_info, n_vcf);
for(i = 0; i < n_chrom; i++) {
my_free(chrom_tab[i].name);
my_free(chrom_tab[i].assembly);
}
my_free(chrom_tab);
my_free(is_lowest);
}
int main(int argc, char **argv) {
ReadSeq read;
gzFile gzf, out_gzf;
long rec_num, line_num, n_err;
int file_num = 0;
char min_qual, max_qual;
char *input_filename, *output_dir, *prefix;
char output_filename[MAX_LINE];
int n_written;
if(argc != 3) {
fprintf(stderr, "usage: %s <fastq_file.txt.gz> <output_dir>\n", argv[0]);
exit(2);
}
input_filename = argv[1];
output_dir = argv[2];
gzf = util_must_gzopen(input_filename, "rb");
prefix = get_prefix(output_dir, input_filename);
rec_num = 0;
line_num = 1;
n_err = 0;
min_qual = max_qual = -1;
out_gzf = NULL;
rec_num = 0;
while(TRUE) {
long r = 0;
r = parse_fastq_read(&read, gzf);
if(r == FASTQ_END) {
/* we have reached the end of the file */
break;
}
if(r == FASTQ_ERR) {
my_warn("%s:%d: invalid fastq record starting on line %ld:\n",
__FILE__, __LINE__, line_num);
n_err += 1;
fprintf(stderr, " %s\n %s\n %s\n %s\n", read.line1,
read.line2, read.line3, read.line4);
}
if(r == FASTQ_OK) {
/* record max and min quality values observed */
if((min_qual == -1) || (min_qual > read.min_qual)) {
min_qual = read.min_qual;
}
if((max_qual == -1) || (max_qual < read.max_qual)) {
max_qual = read.max_qual;
}
if(out_gzf == NULL || rec_num > READS_PER_FILE) {
if(out_gzf) {
/* close old output file */
fprintf(stderr, "\n");
gzclose(out_gzf);
}
file_num += 1;
n_written = snprintf(output_filename, MAX_LINE, "%s.%d.txt.gz",
prefix, file_num);
if(n_written > MAX_LINE) {
my_err("%s:%d: filename too long\n", __FILE__, __LINE__);
}
fprintf(stderr, "writing to file '%s'\n", output_filename);
out_gzf = util_must_gzopen(output_filename, "wb");
rec_num = 0;
}
/* write record to file */
n_written = gzprintf(out_gzf, "%s\n%s\n%s\n%s\n", read.line1,
read.line2, read.line3, read.line4);
if(n_written == 0) {
my_err("%s:%d: failed to write to output file", __FILE__, __LINE__);
}
rec_num += 1;
}
line_num += 4;
if((rec_num % 100000) == 0) {
fprintf(stderr, ".");
}
}
report_qual_type(min_qual, max_qual);
fprintf(stderr, "\n");
fprintf(stderr, "fastq records: written=%ld, errors=%ld\n", rec_num, n_err);
gzclose(gzf);
if(out_gzf) {
gzclose(out_gzf);
}
my_free(prefix);
return 0;
}
/**
* Reads the four lines of the fastq record
*/
static int read_fastq_lines(ReadSeq *read, gzFile f) {
/* read the four lines that make up fastq record */
if(gzgets(f, read->line1, MAX_LINE) == NULL) {
/* end of file */
read->status = FASTQ_END;
read->line1[0] = '\0';
read->line2[0] = '\0';
read->line3[0] = '\0';
read->line4[0] = '\0';
return FASTQ_END;
}
/* check that this line was a header starting with '@' */
if(read->line1[0] != '@') {
my_warn("%s:%d: fastq header line does not start with '@'",
__FILE__, __LINE__);
read->status = FASTQ_ERR;
read->line2[0] = '\0';
read->line3[0] = '\0';
read->line4[0] = '\0';
/* move ahead in file to next line that starts with '@' */
seek_next_header(f);
return read->status;
}
check_line_len(read, read->line1, f);
util_str_rstrip(read->line1);
/* read second line */
if(gzgets(f, read->line2, MAX_LINE) == NULL) {
/* end of file */
my_warn("%s:%d: fastq file ended mid-record\n",
__FILE__, __LINE__);
read->status = FASTQ_ERR;
read->line2[0] = '\0';
read->line3[0] = '\0';
read->line4[0] = '\0';
return FASTQ_ERR;
}
check_line_len(read, read->line2, f);
util_str_rstrip(read->line2);
/* read third line */
if(gzgets(f, read->line3, MAX_LINE) == NULL) {
/* end of file */
my_warn("%s:%d: fastq file ended mid-record\n",
__FILE__, __LINE__);
read->status = FASTQ_ERR;
read->line3[0] = '\0';
read->line4[0] = '\0';
return FASTQ_ERR;
}
check_line_len(read, read->line3, f);
util_str_rstrip(read->line3);
/* read fourth line */
if(gzgets(f, read->line4, MAX_LINE) == NULL) {
/* end of file */
my_warn("%s:%d: fastq file ended mid-record\n", __FILE__, __LINE__);
read->status = FASTQ_ERR;
read->line4[0] = '\0';
return FASTQ_ERR;
}
check_line_len(read, read->line4, f);
util_str_rstrip(read->line4);
return read->status;
}
void vcf_parse_haplotypes(VCFInfo *vcf_info, char *haplotypes,
char *cur) {
int gt_idx, hap1, hap2, i, n;
static int warn_phase = TRUE;
static int warn_parse = TRUE;
long expect_haps, n_haps;
char gt_str[VCF_MAX_FORMAT];
/* char delim[] = " \t"; */
char delim[] = "\t";
char inner_delim[] = ":";
char *inner_cur, *tok, *inner_tok;
/* get index of GT token in format string*/
gt_idx = get_format_index(vcf_info->format, "GT");
if(gt_idx == -1) {
my_err("%s:%d: VCF format string does not specify GT token "
"so cannot obtain haplotypes. Format string: '%s'.\n"
"To use this file, you must run snp2h5 without "
"the --haplotype option.",
__FILE__, __LINE__, vcf_info->format);
}
expect_haps = vcf_info->n_sample * 2;
n_haps = 0;
while((tok = strsep(&cur, delim)) != NULL) {
/* Each genotype string is delimited by ':'
* The GT portions of the string are delimited by '/' or '|'
* '|' indicates phased, '/' indicates unphased.
*/
util_strncpy(gt_str, tok, sizeof(gt_str));
i = 0;
inner_cur = gt_str;
while((i <= gt_idx) && (inner_tok = strsep(&inner_cur, inner_delim)) != NULL) {
if(i == gt_idx) {
n = sscanf(inner_tok, "%d|%d", &hap1, &hap2);
if(n != 2) {
/* try with '/' separator instead */
n = sscanf(inner_tok, "%d/%d", &hap1, &hap2);
if(n == 2) {
if(warn_phase) {
my_warn("%s:%d: some genotypes are unphased (delimited "
"with '/' instead of '|')\n", __FILE__, __LINE__,
inner_tok);
warn_phase = FALSE;
}
} else {
if(warn_parse) {
my_warn("%s:%d: could not parse some genotype "
"strings that look like: '%s'\n", __FILE__, __LINE__,
inner_tok);
warn_parse = FALSE;
}
hap1 = VCF_GTYPE_MISSING;
hap2 = VCF_GTYPE_MISSING;
}
}
if((hap1 != VCF_GTYPE_MISSING && hap1 != 0 && hap1 != 1) ||
(hap2 != VCF_GTYPE_MISSING && hap2 != 0 && hap2 != 1)) {
/* Copy number polymorphisms and multi-allelic SNPs
* can have values other than 0 and 1 (e.g. 3, 4, ...).
* Combined haplotype test does not currently deal with
* these. Set the genotypes to MISSING (-1)
*/
hap1 = VCF_GTYPE_MISSING;
hap2 = VCF_GTYPE_MISSING;
}
if((n_haps + 2) > expect_haps) {
my_err("%s:%d: more genotypes per line than expected",
__FILE__, __LINE__);
}
haplotypes[n_haps] = hap1;
haplotypes[n_haps+1] = hap2;
n_haps += 2;
}
i++;
}
}
if(n_haps != expect_haps) {
my_err("%s:%d: expected %ld genotype values per line, but got "
"%ld", __FILE__, __LINE__, expect_haps, n_haps);
}
}
