int ctx_calls2vcf(int argc, char **argv)
{
const char *in_path = NULL, *out_path = NULL, *out_type = NULL;
// Filtering parameters
int32_t min_mapq = -1, max_align_len = -1, max_allele_len = -1;
// Alignment parameters
int nwmatch = 1, nwmismatch = -2, nwgapopen = -4, nwgapextend = -1;
// ref paths
char const*const* ref_paths = NULL;
size_t nref_paths = 0;
// flank file
const char *sam_path = NULL;
//
// Things we figure out by looking at the input
//
bool isbubble = false;
// samples in VCF, (0 for bubble, does not include ref in breakpoint calls)
size_t i, kmer_size, num_samples;
//
// Reference genome
//
// Hash map of chromosome name -> sequence
ChromHash *genome;
ReadBuffer chroms;
// Arg parsing
char cmd[100];
char shortopts[300];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int c;
// silence error messages from getopt_long
// opterr = 0;
while((c = getopt_long_only(argc, argv, shortopts, longopts, NULL)) != -1) {
cmd_get_longopt_str(longopts, c, cmd, sizeof(cmd));
switch(c) {
case 0: /* flag set */ break;
case 'h': cmd_print_usage(NULL); break;
case 'o': cmd_check(!out_path, cmd); out_path = optarg; break;
case 'O': cmd_check(!out_type, cmd); out_type = optarg; break;
case 'f': cmd_check(!futil_get_force(), cmd); futil_set_force(true); break;
case 'F': cmd_check(!sam_path,cmd); sam_path = optarg; break;
case 'Q': cmd_check(min_mapq < 0,cmd); min_mapq = cmd_uint32(cmd, optarg); break;
case 'A': cmd_check(max_align_len < 0,cmd); max_align_len = cmd_uint32(cmd, optarg); break;
case 'L': cmd_check(max_allele_len < 0,cmd); max_allele_len = cmd_uint32(cmd, optarg); break;
case 'm': nwmatch = cmd_int32(cmd, optarg); break;
case 'M': nwmismatch = cmd_int32(cmd, optarg); break;
case 'g': nwgapopen = cmd_int32(cmd, optarg); break;
case 'G': nwgapextend = cmd_int32(cmd, optarg); break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
die("`"CMD" "SUBCMD" -h` for help. Bad option: %s", argv[optind-1]);
default: ctx_assert2(0, "shouldn't reach here: %c", c);
}
}
// Defaults for unset values
if(out_path == NULL) out_path = "-";
if(max_align_len < 0) max_align_len = DEFAULT_MAX_ALIGN;
if(max_allele_len < 0) max_allele_len = DEFAULT_MAX_ALLELE;
if(optind+2 > argc)
cmd_print_usage("Require <in.txt.gz> and at least one reference");
in_path = argv[optind++];
ref_paths = (char const*const*)argv + optind;
nref_paths = argc - optind;
// These functions call die() on error
gzFile gzin = futil_gzopen(in_path, "r");
// Read call file header
cJSON *json = json_hdr_load(gzin, in_path);
// Check we can handle the kmer size
kmer_size = json_hdr_get_kmer_size(json, in_path);
db_graph_check_kmer_size(kmer_size, in_path);
// Get format (bubble or breakpoint file)
cJSON *json_fmt = json_hdr_get(json, "file_format", cJSON_String, in_path);
if(strcmp(json_fmt->valuestring,"CtxBreakpoints") == 0) isbubble = false;
else if(strcmp(json_fmt->valuestring,"CtxBubbles") == 0) isbubble = true;
else die("Unknown format: '%s'", json_fmt->valuestring);
status("Reading %s in %s format", futil_inpath_str(in_path),
isbubble ? "bubble" : "breakpoint");
if(isbubble) {
// bubble specific
if(sam_path == NULL)
cmd_print_usage("Require -F <flanks.sam> with bubble file");
if(min_mapq < 0) min_mapq = DEFAULT_MIN_MAPQ;
}
else {
// breakpoint specific
if(min_mapq >= 0)
cmd_print_usage("-Q,--min-mapq <Q> only valid with bubble calls");
}
// Open flank file if it exists
htsFile *samfh = NULL;
bam_hdr_t *bam_hdr = NULL;
bam1_t *mflank = NULL;
if(sam_path)
{
if((samfh = hts_open(sam_path, "r")) == NULL)
die("Cannot open SAM/BAM %s", sam_path);
// Load BAM header
bam_hdr = sam_hdr_read(samfh);
if(bam_hdr == NULL) die("Cannot load BAM header: %s", sam_path);
mflank = bam_init1();
}
// Output VCF has 0 samples if bubbles file, otherwise has N where N is
// number of samples/colours in the breakpoint graph
size_t num_graph_samples = json_hdr_get_ncols(json, in_path);
size_t num_graph_nonref = json_hdr_get_nonref_ncols(json, in_path);
num_samples = 0;
if(!isbubble) {
// If last colour has "is_ref", drop number of samples by one
num_samples = num_graph_nonref < num_graph_samples ? num_graph_samples-1
: num_graph_samples;
}
//
// Open output file
//
if(!out_path) out_path = "-";
int mode = vcf_misc_get_outtype(out_type, out_path);
futil_create_output(out_path);
htsFile *vcffh = hts_open(out_path, modes_htslib[mode]);
status("[calls2vcf] Reading %s call file with %zu samples",
isbubble ? "Bubble" : "Breakpoint", num_graph_samples);
status("[calls2vcf] %zu sample output to: %s format: %s",
num_samples, futil_outpath_str(out_path), hsmodes_htslib[mode]);
if(isbubble) status("[calls2vcf] min. MAPQ: %i", min_mapq);
status("[calls2vcf] max alignment length: %i", max_align_len);
status("[calls2vcf] max VCF allele length: %i", max_allele_len);
status("[calls2vcf] alignment match:%i mismatch:%i gap open:%i extend:%i",
nwmatch, nwmismatch, nwgapopen, nwgapextend);
// Load reference genome
read_buf_alloc(&chroms, 1024);
genome = chrom_hash_init();
chrom_hash_load(ref_paths, nref_paths, &chroms, genome);
// convert to upper case
char *s;
for(i = 0; i < chroms.len; i++)
for(s = chroms.b[i].seq.b; *s; s++) *s = toupper(*s);
if(!isbubble) brkpnt_check_refs_match(json, genome, in_path);
bcf_hdr_t *vcfhdr = make_vcf_hdr(json, in_path, !isbubble, kmer_size,
ref_paths, nref_paths,
chroms.b, chroms.len);
if(bcf_hdr_write(vcffh, vcfhdr) != 0) die("Cannot write VCF header");
AlignedCall *call = acall_init();
CallDecomp *aligner = call_decomp_init(vcffh, vcfhdr);
scoring_t *scoring = call_decomp_get_scoring(aligner);
scoring_init(scoring, nwmatch, nwmismatch, nwgapopen, nwgapextend,
false, false, 0, 0, 0, 0);
CallFileEntry centry;
call_file_entry_alloc(¢ry);
char kmer_str[50];
sprintf(kmer_str, ";K%zu", kmer_size);
if(isbubble)
{
// Bubble calls
DecompBubble *bubbles = decomp_bubble_init();
// Set scoring for aligning 3' flank
scoring = decomp_bubble_get_scoring(bubbles);
scoring_init(scoring, nwmatch, nwmismatch, nwgapopen, nwgapextend,
true, true, 0, 0, 0, 0);
while(call_file_read(gzin, in_path, ¢ry)) {
do {
if(sam_read1(samfh, bam_hdr, mflank) < 0)
die("We've run out of SAM entries!");
} while(mflank->core.flag & (BAM_FSECONDARY | BAM_FSUPPLEMENTARY));
// Align call
strbuf_reset(&call->info);
decomp_bubble_call(bubbles, genome, kmer_size, min_mapq,
¢ry, mflank, bam_hdr, call);
strbuf_append_str(&call->info, kmer_str);
acall_decompose(aligner, call, max_align_len, max_allele_len);
}
// print bubble stats
DecompBubbleStats *bub_stats = ctx_calloc(1, sizeof(*bub_stats));
decomp_bubble_cpy_stats(bub_stats, bubbles);
print_bubble_stats(bub_stats);
ctx_free(bub_stats);
decomp_bubble_destroy(bubbles);
}
else
{
// Breakpoint calls
DecompBreakpoint *breakpoints = decomp_brkpt_init();
while(call_file_read(gzin, in_path, ¢ry)) {
strbuf_reset(&call->info);
decomp_brkpt_call(breakpoints, genome, num_samples, ¢ry, call);
strbuf_append_str(&call->info, kmer_str);
acall_decompose(aligner, call, max_align_len, max_allele_len);
}
// print bubble stats
DecompBreakpointStats *brk_stats = ctx_calloc(1, sizeof(*brk_stats));
decomp_brkpt_cpy_stats(brk_stats, breakpoints);
print_breakpoint_stats(brk_stats);
ctx_free(brk_stats);
decomp_brkpt_destroy(breakpoints);
}
// Print stats
DecomposeStats *astats = ctx_calloc(1, sizeof(*astats));
call_decomp_cpy_stats(astats, aligner);
print_acall_stats(astats);
ctx_free(astats);
call_file_entry_dealloc(¢ry);
call_decomp_destroy(aligner);
acall_destroy(call);
// Finished - clean up
cJSON_Delete(json);
gzclose(gzin);
bcf_hdr_destroy(vcfhdr);
hts_close(vcffh);
for(i = 0; i < chroms.len; i++) seq_read_dealloc(&chroms.b[i]);
read_buf_dealloc(&chroms);
chrom_hash_destroy(genome);
if(sam_path) {
hts_close(samfh);
bam_hdr_destroy(bam_hdr);
bam_destroy1(mflank);
}
return EXIT_SUCCESS;
}
static void parse_entries(gzFile gzin, FILE *fout)
{
CallFileEntry centry;
call_file_entry_alloc(¢ry);
ChromPosBuffer chrposbuf;
chrompos_buf_alloc(&chrposbuf, 32);
StrBuf tmpbuf, flank3pbuf;
strbuf_alloc(&tmpbuf, 1024);
strbuf_alloc(&flank3pbuf, 1024);
const char *flank5p, *flank3p;
size_t flank5p_len, flank3p_len;
size_t cpy_flnk_5p, cpy_flnk_3p;
const read_t *chrom = NULL;
size_t ref_start = 0, ref_end = 0;
bool mapped = false, fw_strand = false;
const char **genotypes = NULL;
if(!input_bubble_format)
genotypes = ctx_calloc(num_samples, sizeof(char*));
for(; call_file_read(gzin, input_path, ¢ry); num_entries_read++)
{
size_t nlines = call_file_num_lines(¢ry);
ctx_assert2(!(nlines&1) && nlines >= 6, "Too few lines: %zu", nlines);
flank5p = call_file_get_line(¢ry,1);
flank5p_len = call_file_line_len(¢ry,1);
cpy_flnk_5p = cpy_flnk_3p = 0;
// Read a corresponding SAM entry
if(input_bubble_format)
{
// Trim down alleles, add to 3p flank
bubble_trim_alleles(¢ry, &flank3pbuf);
flank3p = flank3pbuf.b;
flank3p_len = flank3pbuf.end;
mapped = sam_fetch_coords(¢ry, flank5p, flank5p_len, flank3p, flank3p_len,
&cpy_flnk_5p, &cpy_flnk_3p,
&chrom, &ref_start, &ref_end, &fw_strand);
}
else {
flank3p = call_file_get_line(¢ry, 3);
flank3p_len = call_file_line_len(¢ry, 3);
mapped = brkpnt_fetch_coords(¢ry, &chrposbuf,
&chrom, &ref_start, &ref_end, &fw_strand,
&cpy_flnk_5p, &cpy_flnk_3p);
}
if(mapped)
{
// Get call id
const char *hdrline = call_file_get_line(¢ry, 0);
char callid[100];
int r = get_callid_str(hdrline, input_bubble_format, callid, sizeof(callid));
if(r == -1) die("Poorly formatted: %s", hdrline);
if(r == -2) die("Call id string is too long: %s", hdrline);
align_entry(¢ry, callid, flank5p, flank5p_len, flank3p, flank3p_len,
cpy_flnk_5p, cpy_flnk_3p,
chrom, ref_start, ref_end, fw_strand,
&tmpbuf, genotypes,
fout);
}
}
ctx_free(genotypes);
call_file_entry_dealloc(¢ry);
chrompos_buf_dealloc(&chrposbuf);
strbuf_dealloc(&tmpbuf);
strbuf_dealloc(&flank3pbuf);
}