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refactor(phase): write the summary VCF with htslib instead of fprintf (#229) #239

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Merged
TimD1 merged 2 commits into from
Aug 8, 2026
Merged

refactor(phase): write the summary VCF with htslib instead of fprintf (#229) #239

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750e344
refactor(phase): write the summary VCF with htslib instead of fprintf…
TimD1 Aug 8, 2026
1f1165b
fix(tests): reach htslib through variant.h in test_phase.cpp
TimD1 Aug 8, 2026
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81 changes: 31 additions & 50 deletions src/phase.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -24,50 +24,23 @@
* @note Contigs called by only one callset are included; a contig with no query variants has no
* phase block to read, so its truth records are written with PB and BS defaulted
* @throws ERROR if the output summary VCF file cannot be opened for writing
* @throws ERROR if the header or any record cannot be written
* @throws ERROR if neither callset is selected next while variants remain
*/
void phaseblockData::write_summary_vcf(std::string out_vcf_fn) {

// VCF header
if (g.verbosity >= 1) INFO(" Writing summary VCF to '%s'", out_vcf_fn.data());
FILE* out_vcf = fopen(out_vcf_fn.data(), "w");
htsFile* out_vcf = hts_open(out_vcf_fn.data(), "w");
if (out_vcf == NULL) {
ERROR("Failed to open summary VCF file '%s'", out_vcf_fn.data());
}
const std::chrono::time_point<std::chrono::system_clock> now{std::chrono::system_clock::now()};
time_t tt = std::chrono::system_clock::to_time_t(now);
tm local_time = *localtime(&tt);
fprintf(out_vcf, "##fileformat=VCFv4.2\n");
fprintf(out_vcf, "##fileDate=%04d%02d%02d\n", local_time.tm_year + 1900,
local_time.tm_mon + 1, local_time.tm_mday);
fprintf(out_vcf, "##CL=%s\n", g.cmd.data());
for (size_t i = 0; i < this->contigs.size(); i++) {
fprintf(out_vcf, "##contig=<ID=%s,length=%d>\n",
this->contigs[i].data(), this->lengths[i]);
bcf_hdr_t* hdr = summary_vcf_header(this->contigs, this->lengths);
if (bcf_hdr_write(out_vcf, hdr) != 0) {
ERROR("Failed to write summary VCF header to '%s'", out_vcf_fn.data());
}
fprintf(out_vcf, "##FILTER=<ID=PASS,Description=\"All filters passed\">\n");
// The per-haplotype fields carry one value per allele of the sample's GT, which is what VCF
// 4.4's Number=P declares. BCF_VL_P only reaches htslib in 1.23, so a consumer on any older
// bcftools or pysam would report a cardinality error; Number=. produces byte-identical records
// and merely gives up the declared cardinality, so the count and order are stated here instead.
const std::string per_allele = " One value per allele of this sample's GT, in GT allele order, "
"'.' for a reference allele.";
fprintf(out_vcf, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"GenoType\">\n");
fprintf(out_vcf, "##FORMAT=<ID=BD,Number=.,Type=String,Description=\"Benchmark Decision for call (TP/FP/FN).%s\">\n", per_allele.data());
fprintf(out_vcf, "##FORMAT=<ID=BC,Number=.,Type=Float,Description=\"Benchmark Credit (on the interval [0,1], based on sync group edit distance).%s\">\n", per_allele.data());
fprintf(out_vcf, "##FORMAT=<ID=RD,Number=.,Type=Integer,Description=\"Reference edit Distance from truth within current sync group.%s\">\n", per_allele.data());
fprintf(out_vcf, "##FORMAT=<ID=QD,Number=.,Type=Integer,Description=\"Query edit Distance from truth within current sync group.%s\">\n", per_allele.data());
fprintf(out_vcf, "##FORMAT=<ID=BK,Number=.,Type=String,Description=\"BenchmarK category ('gm' if credit == 1, 'lm' if credit > 0, else '.').%s\">\n", per_allele.data());
fprintf(out_vcf, "##FORMAT=<ID=QQ,Number=1,Type=Float,Description=\"variant Quality\">\n");
fprintf(out_vcf, "##FORMAT=<ID=SC,Number=1,Type=Integer,Description=\"SuperCluster (index in contig)\">\n");
fprintf(out_vcf, "##FORMAT=<ID=SG,Number=.,Type=Integer,Description=\"Sync Group (index in supercluster, for credit assignment).%s\">\n", per_allele.data());
fprintf(out_vcf, "##FORMAT=<ID=PS,Number=1,Type=Integer,Description=\"Phase Set identifier (input, per-variant)\">\n");
fprintf(out_vcf, "##FORMAT=<ID=PB,Number=1,Type=Integer,Description=\"Phase Block (output, per-supercluster, index in contig)\">\n");
fprintf(out_vcf, "##FORMAT=<ID=BS,Number=1,Type=Integer,Description=\"Block Phase: 0 = PHASE_KEEP, 1 = PHASE_SWAP)\">\n");
fprintf(out_vcf, "##FORMAT=<ID=VP,Number=1,Type=Integer,Description=\"Variant Phase: 0 = PHASE_ORIG, 1 = PHASE_SWAP, . = PHASE_NONE)\">\n");
fprintf(out_vcf, "##FORMAT=<ID=FE,Number=1,Type=Integer,Description=\"Flip Error (a per-supercluster error)\">\n");
fprintf(out_vcf, "##FORMAT=<ID=GE,Number=1,Type=String,Description=\"Genotype Error ('+' if 0/1 truth -> 1/1 query, '-' if 1/1 truth -> 0/1 query, '.' otherwise)\">\n");
fprintf(out_vcf, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tTRUTH\tQUERY\n");
bcf1_t* rec = bcf_init();
if (rec == NULL) ERROR("Failed to allocate summary VCF record");

// write variants
for (std::string ctg : this->contigs) {
Expand Down Expand Up @@ -133,7 +106,7 @@ void phaseblockData::write_summary_vcf(std::string out_vcf_fn) {
phase_block++;

/* if (next[QUERY] && ptrs[QUERY] < qvars->n) { */
/* fprintf(out_vcf, "orig_gt: %s\tmatched_gt: %s\tcredit: %.2f|%.2f\tref_dist: %d|%d\tphase: %s\n", */
/* fprintf(stderr, "orig_gt: %s\tmatched_gt: %s\tcredit: %.2f|%.2f\tref_dist: %d|%d\tphase: %s\n", */
/* gt_strs[vars[QUERY]->orig_gts[ptrs[QUERY]]].data(), */
/* gt_strs[vars[QUERY]->matched_gts[ptrs[QUERY]]].data(), */
/* vars[QUERY]->credit[HAP1][ptrs[QUERY]], */
Expand All @@ -144,39 +117,47 @@ void phaseblockData::write_summary_vcf(std::string out_vcf_fn) {
/* ); */
/* } */
/* if (next[TRUTH] && ptrs[TRUTH] < tvars->n) { */
/* fprintf(out_vcf, "orig_gt: %s\n", */
/* fprintf(stderr, "orig_gt: %s\n", */
/* gt_strs[vars[TRUTH]->orig_gts[ptrs[TRUTH]]].data()); */
/* } */

bcf_clear(rec);
if (next[QUERY]) {
// a positional tie between differing alleles is not a match: the two are written as
// co-located records, the truth one on the next pass
bool matched = next[TRUTH] &&
vars[QUERY]->refs[ptrs[QUERY]] == vars[TRUTH]->refs[ptrs[TRUTH]] &&
vars[QUERY]->alts[ptrs[QUERY]] == vars[TRUTH]->alts[ptrs[TRUTH]];
vars[QUERY]->print_var_info(out_vcf, this->ref, ctg, ptrs[QUERY]);
if (matched) {
vars[TRUTH]->print_var_sample(out_vcf, ptrs[TRUTH],
sc_idx, phase_block, block_state == PHASE_SWAP, flip_error);
} else {
vars[TRUTH]->print_var_empty(out_vcf, sc_idx, phase_block);
}
vars[QUERY]->print_var_sample(out_vcf, ptrs[QUERY],
sc_idx, phase_block, block_state == PHASE_SWAP, flip_error, true);
vars[QUERY]->set_var_record(hdr, rec, this->ref, ctg, ptrs[QUERY]);
set_record_samples(hdr, rec,
matched ? vars[TRUTH]->var_sample_fields(ptrs[TRUTH], sc_idx, phase_block,
block_state == PHASE_SWAP, flip_error) :
empty_sample_fields(sc_idx, phase_block),
vars[QUERY]->var_sample_fields(ptrs[QUERY], sc_idx, phase_block,
block_state == PHASE_SWAP, flip_error, true));
ptrs[QUERY]++;
if (matched) ptrs[TRUTH]++;
} else if (next[TRUTH]) {
vars[TRUTH]->print_var_info(out_vcf, this->ref, ctg, ptrs[TRUTH]);
vars[TRUTH]->print_var_sample(out_vcf, ptrs[TRUTH],
sc_idx, phase_block, block_state == PHASE_SWAP, flip_error);
vars[QUERY]->print_var_empty(out_vcf, sc_idx, phase_block, true);
vars[TRUTH]->set_var_record(hdr, rec, this->ref, ctg, ptrs[TRUTH]);
set_record_samples(hdr, rec,
vars[TRUTH]->var_sample_fields(ptrs[TRUTH], sc_idx, phase_block,
block_state == PHASE_SWAP, flip_error),
empty_sample_fields(sc_idx, phase_block));
ptrs[TRUTH]++;
} else {
ERROR("No variants are selected next.");
}
if (bcf_write(out_vcf, hdr, rec) != 0) {
ERROR("Failed to write summary VCF record at %s:%lld", ctg.data(),
static_cast<long long>(rec->pos+1));
}
}
}
fclose(out_vcf);
bcf_destroy(rec);
bcf_hdr_destroy(hdr);
if (hts_close(out_vcf) != 0) {
ERROR("Failed to close summary VCF file '%s'", out_vcf_fn.data());
}
}


Expand Down
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