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a5 patch
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@chrchang
chrchang committed Nov 24, 2024
1 parent 56a8552 commit bb0f4d4
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Showing 4 changed files with 81 additions and 33 deletions.
4 changes: 2 additions & 2 deletions 2.0/plink2.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
namespace plink2 {
#endif

static const char ver_str[] = "PLINK v2.0.0-a.5.18"
static const char ver_str[] = "PLINK v2.0.0-a.5.19"
#ifdef NOLAPACK
"NL"
#elif defined(LAPACK_ILP64)
Expand Down Expand Up @@ -72,7 +72,7 @@ static const char ver_str[] = "PLINK v2.0.0-a.5.18"
#elif defined(USE_AOCL)
" AMD"
#endif
" (11 Nov 2024)";
" (24 Nov 2024)";
static const char ver_str2[] =
// include leading space if day < 10, so character length stays the same
""
Expand Down
6 changes: 3 additions & 3 deletions 2.0/plink2_data.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -3748,7 +3748,7 @@ PglErr WriteBimSplit(const char* outname, const uintptr_t* variant_include, cons
if (varid_dup) {
for (uint32_t uii = 0; uii != varid_templatep->insert_ct; ++uii) {
const uint32_t insert_type = varid_templatep->insert_types[uii];
if ((insert_type == 3) || ((insert_type == 2) && (varid_templatep->alleles_needed & 4))) {
if ((insert_type == 3) || ((insert_type == 2) && (varid_templatep->allele_flags & kfVaridTemplateAlleleAsciiOrder))) {
// Could define what takes precedence here, but simpler to prohibit
// this combination.
logerrputs("Error: 'vid-[split-]dup' cannot be used with a --set-all-var-ids or\n--set-missing-var-ids template string containing a non-REF allele.\n");
Expand Down Expand Up @@ -4051,7 +4051,7 @@ PglErr WritePvarSplit(const char* outname, const uintptr_t* variant_include, con
if (varid_dup) {
for (uint32_t uii = 0; uii != varid_templatep->insert_ct; ++uii) {
const uint32_t insert_type = varid_templatep->insert_types[uii];
if ((insert_type == 3) || ((insert_type == 2) && (varid_templatep->alleles_needed & 4))) {
if ((insert_type == 3) || ((insert_type == 2) && (varid_templatep->allele_flags & kfVaridTemplateAlleleAsciiOrder))) {
// Could define what takes precedence here, but simpler to prohibit
// this combination.
logerrputs("Error: 'vid-[split-]dup' cannot be used with a --set-all-var-ids or\n--set-missing-var-ids template string containing a non-REF allele.\n");
Expand Down Expand Up @@ -4691,7 +4691,7 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons
if (varid_dup) {
for (uint32_t uii = 0; uii != varid_templatep->insert_ct; ++uii) {
const uint32_t insert_type = varid_templatep->insert_types[uii];
if ((insert_type == 3) || ((insert_type == 2) && (varid_templatep->alleles_needed & 4))) {
if ((insert_type == 3) || ((insert_type == 2) && (varid_templatep->allele_flags & kfVaridTemplateAlleleAsciiOrder))) {
// Could define what takes precedence here, but simpler to prohibit
// this combination.
logerrputs("Error: 'vid-[split-]dup' cannot be used with a --set-all-var-ids or\n--set-missing-var-ids template string containing a non-REF allele.\n");
Expand Down
95 changes: 68 additions & 27 deletions 2.0/plink2_pvar.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -185,20 +185,24 @@ PglErr ReadChrsetHeaderLine(const char* chrset_iter, const char* file_descrip, M
return reterr;
}

static_assert(kfVaridTemplateAlleleRefOr1 == 1, "VaridTemplateInit() or VaridTemplateAlleleFlags needs to be updated.");
static_assert(kfVaridTemplateAlleleAltOr2 == 2, "VaridTemplateInit() or VaridTemplateAlleleFlags needs to be updated.");
void VaridTemplateInit(const char* varid_template_str, const char* missing_id_match, char* chr_output_name_buf, uint32_t new_id_max_allele_slen, uint32_t overflow_substitute_blen, VaridTemplate* vtp) {
// template string was previously validated
// varid_template is only input, everything else is output values
const char* varid_template_str_iter = varid_template_str;
uint32_t template_insert_ct = 0;
uint32_t template_base_len = 0;
uint32_t alleles_needed = 0; // bit 0 = ref, bit 1 = alt, bit 2 = ascii sort
VaridTemplateAlleleFlags allele_flags = kfVaridTemplateAllele0;
vtp->chr_output_name_buf = chr_output_name_buf;
vtp->segs[0] = varid_template_str_iter;
vtp->chr_slen = 0;
for (unsigned char ucc = *varid_template_str_iter; ucc; ucc = *(++varid_template_str_iter)) {
if (ucc > '@') {
continue;
}
// VaridTemplateIsValid() ensures ucc is in {'$', '1', '2', 'A', 'R', 'a',
// 'r'}.
uint32_t seg_len;
uint32_t insert_type;
if (ucc == '@') {
Expand All @@ -211,16 +215,16 @@ void VaridTemplateInit(const char* varid_template_str, const char* missing_id_ma
continue;
} else {
seg_len = varid_template_str_iter - vtp->segs[template_insert_ct];
const uint32_t uii = ctou32(*(++varid_template_str_iter));
if (uii <= '2') {
alleles_needed += 2; // this happens twice
insert_type = uii - 48; // '1' -> type 2, '2' -> type 3
const uint32_t char_code = ctou32(*(++varid_template_str_iter));
uint32_t flagbit; // 1 if '1' or 'R'/'r', 2 if '2' or 'A'/'a'
if (char_code <= '2') {
allele_flags |= kfVaridTemplateAlleleAsciiOrder;
flagbit = char_code - 48;
} else {
// 'r' -> type 2, 'a' -> type 3
insert_type = 1 + ((uii & 0xdf) == 'A');
flagbit = 1 + ((char_code & 0xdf) == 'A');
}
alleles_needed += insert_type;
++insert_type;
allele_flags |= S_CAST(VaridTemplateAlleleFlags, flagbit);
insert_type = flagbit + 1;
}
vtp->seg_lens[template_insert_ct] = seg_len;
template_base_len += seg_len;
Expand All @@ -231,25 +235,35 @@ void VaridTemplateInit(const char* varid_template_str, const char* missing_id_ma
vtp->seg_lens[template_insert_ct] = seg_len;
vtp->insert_ct = template_insert_ct;
vtp->base_len = template_base_len + seg_len;
vtp->alleles_needed = alleles_needed;
vtp->allele_flags = allele_flags;
vtp->new_id_max_allele_slen = new_id_max_allele_slen;
vtp->overflow_substitute_blen = overflow_substitute_blen;
vtp->missing_id_match = missing_id_match;
}

// alt1_end currently allowed to be nullptr in biallelic case
BoolErr VaridTemplateApply(unsigned char* tmp_alloc_base, const VaridTemplate* vtp, const char* ref_start, const char* alt1_start, uint32_t cur_bp, uint32_t ref_token_slen, uint32_t extra_alt_ct, uint32_t alt_token_slen, unsigned char** tmp_alloc_endp, uintptr_t* new_id_allele_len_overflowp, uint32_t* id_slen_ptr) {
// (insert_ptrs[x], insert_slens[x]) is the (start, slen) of the
// insert-segment of type x:
// 0: chromosome
// 1: 1-based position
// 2: $r or $1
// 3: $a or $2
// Types 0 and 1 are always present, but 2 and/or 3 can be missing.
uint32_t insert_slens[4];
const uint32_t alleles_needed = vtp->alleles_needed;
const VaridTemplateAlleleFlags allele_flags = vtp->allele_flags;
const uint32_t new_id_max_allele_slen = vtp->new_id_max_allele_slen;
uint32_t id_slen = UintSlen(cur_bp);
insert_slens[0] = vtp->chr_slen;
insert_slens[1] = id_slen;
id_slen += vtp->base_len;
const uint32_t ref_or_1_exists = (allele_flags & kfVaridTemplateAlleleRefOr1)? 1 : 0;
uint32_t ref_slen = 0;
uint32_t cur_overflow = 0;
const char* tmp_allele_ptrs[2];
if (alleles_needed & 1) {
const char* tmp_allele_ptrs[2]; // [0] = RefOr1, [1] = AltOr2
tmp_allele_ptrs[0] = nullptr;
tmp_allele_ptrs[1] = nullptr; // maybe-uninitialized warning
if (ref_or_1_exists) {
ref_slen = ref_token_slen;
if (ref_slen > new_id_max_allele_slen) {
ref_slen = new_id_max_allele_slen;
Expand All @@ -259,7 +273,7 @@ BoolErr VaridTemplateApply(unsigned char* tmp_alloc_base, const VaridTemplate* v
id_slen += ref_slen;
tmp_allele_ptrs[0] = ref_start;
}
if (alleles_needed > 1) {
if (allele_flags & (kfVaridTemplateAlleleAltOr2 | kfVaridTemplateAlleleAsciiOrder)) {
uint32_t alt1_slen;
if (!extra_alt_ct) {
alt1_slen = alt_token_slen;
Expand All @@ -271,7 +285,7 @@ BoolErr VaridTemplateApply(unsigned char* tmp_alloc_base, const VaridTemplate* v
++cur_overflow;
}
id_slen += alt1_slen;
if (alleles_needed <= 3) {
if (!(allele_flags & kfVaridTemplateAlleleAsciiOrder)) {
VaridTemplateApply_keep_allele_ascii_order:
insert_slens[3] = alt1_slen;
tmp_allele_ptrs[1] = alt1_start;
Expand Down Expand Up @@ -316,8 +330,16 @@ BoolErr VaridTemplateApply(unsigned char* tmp_alloc_base, const VaridTemplate* v
// maybe-uninitialized warnings
insert_ptrs[0] = nullptr;
insert_ptrs[1] = nullptr;
insert_ptrs[2] = nullptr;

insert_ptrs[2] = nullptr;
insert_ptrs[3] = nullptr;
// insert_ct currently guaranteed to be >= 2 since @ and # required
// insert_ct > 2 possibilities:
// $r without $a: insert_ct=3, use tmp_allele_ptrs[0] and insert_slens[2]
// $a without $r: insert_ct=3, use tmp_allele_ptrs[1] and insert_slens[3]
// (fixed bug on 24 Nov 2024)
// $r+$a or $1+$2: insert_ct=4, use (tmp_allele_ptrs[0], insert_slens[2])
// followed by (tmp_allele_ptrs[1], insert_slens[3])
for (uint32_t insert_idx = 0; insert_idx != insert_ct; ++insert_idx) {
id_iter = memcpya(id_iter, vtp->segs[insert_idx], vtp->seg_lens[insert_idx]);
const uint32_t cur_insert_type = vtp->insert_types[insert_idx];
Expand All @@ -328,9 +350,15 @@ BoolErr VaridTemplateApply(unsigned char* tmp_alloc_base, const VaridTemplate* v

memcpy(insert_ptrs[0], vtp->chr_output_name_buf, insert_slens[0]);
u32toa(cur_bp, insert_ptrs[1]);
// insert_ct currently guaranteed to be >= 2 since @ and # required
for (uint32_t insert_type_idx = 2; insert_type_idx != insert_ct; ++insert_type_idx) {
memcpy(insert_ptrs[insert_type_idx], tmp_allele_ptrs[insert_type_idx - 2], insert_slens[insert_type_idx]);
if (insert_ct > 2) {
for (uint32_t insert_type_idx = 2; insert_type_idx != 4; ++insert_type_idx) {
char* cur_dst = insert_ptrs[insert_type_idx];
if (cur_dst == nullptr) {
// bugfix (24 Nov 2024)
continue;
}
memcpy(cur_dst, tmp_allele_ptrs[insert_type_idx - 2], insert_slens[insert_type_idx]);
}
}
}
*id_slen_ptr = id_slen;
Expand All @@ -342,16 +370,19 @@ BoolErr VaridTemplateApply(unsigned char* tmp_alloc_base, const VaridTemplate* v
// Probable todo: pull out the common parts of the functions.
char* VaridTemplateWrite(const VaridTemplate* vtp, const char* ref_start, const char* alt1_start, uint32_t cur_bp, uint32_t ref_token_slen, uint32_t extra_alt_ct, uint32_t alt_token_slen, char* dst) {
uint32_t insert_slens[4];
const uint32_t alleles_needed = vtp->alleles_needed;
const uint32_t allele_flags = vtp->allele_flags;
const uint32_t new_id_max_allele_slen = vtp->new_id_max_allele_slen;
uint32_t id_slen = UintSlen(cur_bp);
insert_slens[0] = vtp->chr_slen;
insert_slens[1] = id_slen;
id_slen += vtp->base_len;
const uint32_t ref_or_1_exists = (allele_flags & kfVaridTemplateAlleleRefOr1)? 1 : 0;
uint32_t ref_slen = 0;
uint32_t cur_overflow = 0;
const char* tmp_allele_ptrs[2];
if (alleles_needed & 1) {
tmp_allele_ptrs[0] = nullptr;
tmp_allele_ptrs[1] = nullptr;
if (ref_or_1_exists) {
ref_slen = ref_token_slen;
if (ref_slen > new_id_max_allele_slen) {
ref_slen = new_id_max_allele_slen;
Expand All @@ -361,7 +392,7 @@ char* VaridTemplateWrite(const VaridTemplate* vtp, const char* ref_start, const
id_slen += ref_slen;
tmp_allele_ptrs[0] = ref_start;
}
if (alleles_needed > 1) {
if (allele_flags & (kfVaridTemplateAlleleAltOr2 | kfVaridTemplateAlleleAsciiOrder)) {
uint32_t alt1_slen;
if (!extra_alt_ct) {
alt1_slen = alt_token_slen;
Expand All @@ -373,7 +404,7 @@ char* VaridTemplateWrite(const VaridTemplate* vtp, const char* ref_start, const
cur_overflow = 1;
}
id_slen += alt1_slen;
if (alleles_needed <= 3) {
if (!(allele_flags & kfVaridTemplateAlleleAsciiOrder)) {
VaridTemplateWrite_keep_allele_ascii_order:
insert_slens[3] = alt1_slen;
tmp_allele_ptrs[1] = alt1_start;
Expand Down Expand Up @@ -407,7 +438,9 @@ char* VaridTemplateWrite(const VaridTemplate* vtp, const char* ref_start, const
// maybe-uninitialized warnings
insert_ptrs[0] = nullptr;
insert_ptrs[1] = nullptr;

insert_ptrs[2] = nullptr;
insert_ptrs[3] = nullptr;

for (uint32_t insert_idx = 0; insert_idx != insert_ct; ++insert_idx) {
id_iter = memcpya(id_iter, vtp->segs[insert_idx], vtp->seg_lens[insert_idx]);
Expand All @@ -419,16 +452,24 @@ char* VaridTemplateWrite(const VaridTemplate* vtp, const char* ref_start, const

memcpy(insert_ptrs[0], vtp->chr_output_name_buf, insert_slens[0]);
u32toa(cur_bp, insert_ptrs[1]);
// insert_ct currently guaranteed to be >= 2 since @ and # required
for (uint32_t insert_type_idx = 2; insert_type_idx != insert_ct; ++insert_type_idx) {
memcpy(insert_ptrs[insert_type_idx], tmp_allele_ptrs[insert_type_idx - 2], insert_slens[insert_type_idx]);
if (insert_ct > 2) {
for (uint32_t insert_type_idx = 2; insert_type_idx != 4; ++insert_type_idx) {
char* cur_dst = insert_ptrs[insert_type_idx];
if (cur_dst == nullptr) {
continue;
}
memcpy(cur_dst, tmp_allele_ptrs[insert_type_idx - 2], insert_slens[insert_type_idx]);
}
}
return id_end;
}

uint32_t VaridWorstCaseSlen(const VaridTemplate* vtp, uint32_t max_chr_slen, uint32_t max_allele_slen) {
const VaridTemplateAlleleFlags allele_flags = vtp->allele_flags;
uint32_t allele_ct = (allele_flags & kfVaridTemplateAlleleRefOr1)? 1 : 0;
allele_ct += (allele_flags & kfVaridTemplateAlleleAltOr2)? 1 : 0;
// +10 for base-pair coordinate
return (max_allele_slen * vtp->alleles_needed + vtp->base_len + max_chr_slen + 10);
return (max_allele_slen * allele_ct + vtp->base_len + max_chr_slen + 10);
}

void BackfillChrIdxs(const ChrInfo* cip, uint32_t chrs_encountered_m1, uint32_t offset, uint32_t end_vidx, ChrIdx* chr_idxs) {
Expand Down
9 changes: 8 additions & 1 deletion 2.0/plink2_pvar.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,13 @@ namespace plink2 {

PglErr ReadChrsetHeaderLine(const char* chrset_iter, const char* file_descrip, MiscFlags misc_flags, uintptr_t line_idx, ChrInfo* cip);

FLAGSET_DEF_START()
kfVaridTemplateAllele0,
kfVaridTemplateAlleleRefOr1 = (1 << 0),
kfVaridTemplateAlleleAltOr2 = (1 << 1),
kfVaridTemplateAlleleAsciiOrder = (1 << 2)
FLAGSET_DEF_END(VaridTemplateAlleleFlags);

typedef struct VaridTemplateStruct {
NONCOPYABLE(VaridTemplateStruct);
const char* missing_id_match;
Expand All @@ -71,7 +78,7 @@ typedef struct VaridTemplateStruct {
uint32_t insert_ct;
uint32_t base_len;
uint32_t chr_slen;
uint32_t alleles_needed;
VaridTemplateAlleleFlags allele_flags;

// next two values (and the first two) are common between templates
uint32_t new_id_max_allele_slen;
Expand Down

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