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backport --lax-bgen-import
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@chrchang
chrchang committed Oct 5, 2024
1 parent d8fcfe0 commit 009b7eb
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Showing 4 changed files with 52 additions and 15 deletions.
6 changes: 6 additions & 0 deletions 2.0/plink2.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -7134,6 +7134,12 @@ int main(int argc, char** argv) {
} else if (strequal_k_unsafe(flagname_p2, "ax-chrx-import")) {
import_flags |= kfImportLaxChrX;
goto main_param_zero;
} else if (strequal_k_unsafe(flagname_p2, "ax-bgen-import")) {
if (unlikely(!(xload & kfXloadOxBgen))) {
logerrputs("Error: --lax-bgen-import must be used with --bgen.\n");
goto main_ret_INVALID_CMDLINE_A;
}
import_flags |= kfImportLaxBgen;
} else if (likely(strequal_k_unsafe(flagname_p2, "d"))) {
if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 2, 4))) {
goto main_ret_INVALID_CMDLINE_2A;
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3 changes: 2 additions & 1 deletion 2.0/plink2_data.h
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,8 @@ FLAGSET_DEF_START()
kfImportVcfRequireGt = (1 << 3),
kfImportVcfRefNMissing = (1 << 4),
kfImportLaxChrX = (1 << 5),
kfImportVcfAllowNoNonvar = (1 << 8)
kfImportVcfAllowNoNonvar = (1 << 8),
kfImportLaxBgen = (1 << 9)
FLAGSET_DEF_END(ImportFlags);

CONSTI32(kMaxInfoKeySlen, kMaxIdSlen);
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5 changes: 5 additions & 0 deletions 2.0/plink2_help.cc
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Expand Up @@ -1636,6 +1636,11 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {
" --oxford-single-chr <chr name> : Specify single-chromosome .gen/.bgen file\n"
" with no useful chromosome info inside.\n"
);
HelpPrint("lax-bgen-import\0bgen\0", &help_ctrl, 0,
" --lax-bgen-import : Do not error out when .bgen header has an\n"
" overstated variant count (possible from\n"
" IMPUTE5).\n"
);
HelpPrint("missing-code\0missing_code\0data\0sample\0", &help_ctrl, 0,
" --missing-code [string list] : Comma-delimited list of missing phenotype\n"
" (alias: --missing_code) values for Oxford-format import (default\n"
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53 changes: 39 additions & 14 deletions 2.0/plink2_import.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -12151,10 +12151,8 @@ PglErr OxBgenToPgen(const char* bgenname, const char* samplename, const char* co
logerrputs("Error: Invalid .bgen magic number.\n");
goto OxBgenToPgen_ret_MALFORMED_INPUT;
}
// Don't want to print "Empty .bgen file" error message when magic number
// is wrong.
const uint32_t raw_variant_ct = initial_uints[2];
if (unlikely(!raw_variant_ct)) {
const uint32_t header_variant_ct = initial_uints[2];
if (unlikely(!header_variant_ct)) {
logerrputs("Error: Empty .bgen file.\n");
goto OxBgenToPgen_ret_DEGENERATE_DATA;
}
Expand All @@ -12180,7 +12178,8 @@ PglErr OxBgenToPgen(const char* bgenname, const char* samplename, const char* co
logerrputs("Error: Invalid .bgen header.\n");
goto OxBgenToPgen_ret_MALFORMED_INPUT;
}
logprintf("--bgen: %u variant%s detected, format v1.%c.\n", raw_variant_ct, (raw_variant_ct == 1)? "" : "s", (layout == 1)? '1' : ((compression_mode == 2)? '3' : '2'));
logprintf("--bgen: %u variant%s declared in header, format v1.%c.\n", header_variant_ct, (header_variant_ct == 1)? "" : "s", (layout == 1)? '1' : ((compression_mode == 2)? '3' : '2'));
uint32_t raw_variant_ct = header_variant_ct;
if (samplename[0]) {
uint32_t sfile_sample_ct;
reterr = OxSampleToPsam(samplename, const_fid, ox_missing_code, missing_catname, misc_flags, import_flags, psam_01, id_delim, outname, outname_end, &sfile_sample_ct);
Expand Down Expand Up @@ -12431,6 +12430,8 @@ PglErr OxBgenToPgen(const char* bgenname, const char* samplename, const char* co
// true for both provisional-reference and real-reference second
const uint32_t prov_ref_allele_second = !(oxford_import_flags & kfOxfordImportRefFirst);

const uint32_t allow_overstated_variant_ct = (import_flags / kfImportLaxBgen) & 1;

if (hard_call_thresh == UINT32_MAX) {
hard_call_thresh = kDosageMid / 10;
}
Expand Down Expand Up @@ -12496,8 +12497,8 @@ PglErr OxBgenToPgen(const char* bgenname, const char* samplename, const char* co
// (well, it didn't before libdeflate, anyway. recheck this.)
calc_thread_ct = 2;
}
if (calc_thread_ct > raw_variant_ct) {
calc_thread_ct = raw_variant_ct;
if (calc_thread_ct > header_variant_ct) {
calc_thread_ct = header_variant_ct;
}
if (unlikely(bigstack_alloc_u16p(calc_thread_ct, &scan_ctx.bgen_geno_bufs))) {
goto OxBgenToPgen_ret_NOMEM;
Expand Down Expand Up @@ -12575,10 +12576,21 @@ PglErr OxBgenToPgen(const char* bgenname, const char* samplename, const char* co
unsigned char** compressed_geno_starts = common.compressed_geno_starts[0];
unsigned char* bgen_geno_iter = compressed_geno_bufs[0];
uint32_t skip = 0;
for (uint32_t variant_uidx = 0; variant_uidx != raw_variant_ct; ) {
for (uint32_t variant_uidx = 0; variant_uidx != header_variant_ct; ) {
uint32_t uii;
if (unlikely(!fread_unlocked(&uii, 4, 1, bgenfile))) {
goto OxBgenToPgen_ret_READ_FAIL;
{
const uintptr_t bytes_read = fread_unlocked(&uii, 1, 4, bgenfile);
if (bytes_read != 4) {
// don't know of a bgen-1.1 use case, but may as well make
// --lax-bgen-import have a consistent effect.
if (likely(allow_overstated_variant_ct && (!bytes_read))) {
raw_variant_ct = variant_uidx;
putc_unlocked('\n', stdout);
logprintf("--lax-bgen-import: .bgen file actually contains %u variant%s.\n", raw_variant_ct, (raw_variant_ct == 1)? "" : "s");
break;
}
goto OxBgenToPgen_ret_READ_FAIL;
}
}
if (unlikely(uii != sample_ct)) {
logputs("\n");
Expand Down Expand Up @@ -12704,7 +12716,7 @@ PglErr OxBgenToPgen(const char* bgenname, const char* samplename, const char* co
if (dosage_exists) {
// don't need to scan for any more dosages
StopThreads(&tg);
if (!chr_filter_exists) {
if ((!chr_filter_exists) && (!allow_overstated_variant_ct)) {
break;
}
continue;
Expand Down Expand Up @@ -13248,14 +13260,27 @@ PglErr OxBgenToPgen(const char* bgenname, const char* samplename, const char* co
// temporary kludge
uint32_t multiallelic_skip_ct = 0;

for (uint32_t variant_uidx = 0; variant_uidx != raw_variant_ct; ) {
for (uint32_t variant_uidx = 0; variant_uidx != header_variant_ct; ) {
// format is mostly identical to bgen 1.1; but there's no sample count,
// and there is an allele count
// logic is more similar to the second bgen 1.1 pass since we write the
// .pvar here.
uint16_t snpid_slen;
if (unlikely(!fread_unlocked(&snpid_slen, 2, 1, bgenfile))) {
goto OxBgenToPgen_ret_READ_FAIL;
{
const uintptr_t bytes_read = fread_unlocked(&snpid_slen, 1, 2, bgenfile);
if (bytes_read != 2) {
if (likely(!bytes_read)) {
putc_unlocked('\n', stdout);
if (likely(allow_overstated_variant_ct)) {
raw_variant_ct = variant_uidx;
logprintf("--lax-bgen-import: .bgen file actually contains %u variant%s.\n", raw_variant_ct, (raw_variant_ct == 1)? "" : "s");
break;
}
logerrprintfww("Error: .bgen file actually contains %u variant%s; header is incorrect. Add --lax-bgen-import to force import.\n", variant_uidx, (variant_uidx == 1)? "" : "s");
goto OxBgenToPgen_ret_INCONSISTENT_INPUT;
}
goto OxBgenToPgen_ret_READ_FAIL;
}
}
char* rsid_start = R_CAST(char*, loadbuf);
if (!snpid_chr) {
Expand Down

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