/**
* @param cpy_flnk_5p how many characters to copy from end of 5' flank to start of allele
* @param cpy_flnk_3p how many characters to copy from end of 3' flank to end of allele
*/
static void align_entry_allele(const char *line, size_t linelen,
const char *flank5p, size_t flank5p_len,
const char *flank3p, size_t flank3p_len,
size_t cpy_flnk_5p, size_t cpy_flnk_3p,
const read_t *chr,
size_t ref_start, size_t ref_end,
bool fw_strand,
const char *info, const char **genotypes,
StrBuf *tmpbuf, FILE *fout)
{
(void)flank3p_len;
ctx_assert(ref_start <= ref_end);
// Ref allele
const char *ref_allele = chr->seq.b + ref_start;
size_t ref_len = ref_end-ref_start;
// Construct alt allele
const char *alt_allele;
size_t alt_len;
if(cpy_flnk_5p + cpy_flnk_3p == 0 && fw_strand)
{
alt_allele = line;
alt_len = linelen;
}
else
{
strbuf_reset(tmpbuf);
strbuf_append_strn(tmpbuf, flank5p+flank5p_len-cpy_flnk_5p, cpy_flnk_5p);
strbuf_append_strn(tmpbuf, line, linelen);
strbuf_append_strn(tmpbuf, flank3p, cpy_flnk_3p);
if(!fw_strand) dna_revcomp_str(tmpbuf->b, tmpbuf->b, tmpbuf->end);
alt_allele = tmpbuf->b;
alt_len = tmpbuf->end;
}
// printf("%.*s vs %.*s\n", (int)(ref_end-ref_start), chr->seq.b + ref_start,
// (int)alt_len, seq);
// Align chrom and seq
needleman_wunsch_align2(ref_allele, alt_allele, ref_len, alt_len,
&nw_scoring_allele, nw_aligner, aln);
num_nw_allele++;
// Break into variants and print VCF
align_biallelic(aln->result_a, aln->result_b,
chr, ref_start,
info, genotypes, fout);
}
void acall_decompose(CallDecomp *dc, const AlignedCall *call,
size_t max_line_len, size_t max_allele_len)
{
dc->stats.ncalls++;
if(call->chrom == NULL) { return; }
dc->stats.ncalls_mapped++;
const read_t *chrom = call->chrom;
const char *ref_allele = chrom->seq.b + call->start;
size_t i, ref_len = call->end - call->start;
const StrBuf *alt;
ctx_assert2(call->start <= call->end, "%u .. %u", call->start, call->end);
if(ref_len > max_line_len) {
dc->stats.ncalls_ref_allele_too_long++;
return; // can't align
}
dc->stats.nlines += call->n_lines;
// printf("chr:%s %u - %u\n", call->chrom->name.b, call->start, call->end);
for(i = 0; i < call->n_lines; i++)
{
alt = &call->lines[i];
ctx_assert(strlen(alt->b) == alt->end);
// Quick check if sequence too long or are matching
if(alt->end > max_line_len) {
dc->stats.nlines_too_long++;
} else if(ref_len == alt->end && strncasecmp(ref_allele, alt->b, ref_len) == 0) {
dc->stats.nlines_match_ref++;
} else {
// printf("REF: '%*.s' [%zu]\n", (int)ref_len, ref_allele, ref_len);
// printf("ALT: '%*.s' [%zu]\n", (int)alt->end, alt->b, alt->end);
needleman_wunsch_align2(ref_allele, alt->b, ref_len, alt->end,
dc->scoring, dc->nw_aligner, dc->aln);
// printf("ALNA: %s\n", dc->aln->result_a);
// printf("ALNB: %s\n", dc->aln->result_b);
align_biallelic(dc->aln->result_a, dc->aln->result_b, chrom,
call->gts+i*call->n_samples, call->n_samples,
dc, call, max_allele_len);
dc->stats.nlines_mapped++;
}
}
}
