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ugly patches for __MINGW64__
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@zhanxw
zhanxw committed Nov 28, 2023
1 parent f050002 commit 5d728c1
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Showing 7 changed files with 135 additions and 58 deletions.
2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ Package: seqminer
Type: Package
Title: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into R
Version: 9.2
Version: 9.3
Date: 2023-11-18
Authors@R: c(person("Xiaowei", "Zhan", email = "zhanxw@gmail.com", role = c("aut", "cre")),
person("Dajiang", "Liu", email = "dajiang.liu@gmail.com", role = "aut"),
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5 changes: 4 additions & 1 deletion src/PlinkInputFile.h
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Expand Up @@ -97,8 +97,11 @@ class PlinkInputFile{
}
};
delete lr;

#ifndef __MINGW64__
REprintf("Finished loading %s. %zu chrom, %zu indv\n", fnPrefix, snp2Idx.size(), indv.size());
#else
REprintf("Finished loading %s. %lu chrom, %lu indv\n", fnPrefix, (unsigned long int) snp2Idx.size(), (unsigned long int) indv.size());
#endif
}
~PlinkInputFile() {
fclose(this->fpBed);
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5 changes: 5 additions & 0 deletions src/R_CPP_interface.cpp
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
#include "R_CPP_interface.h"

#include "TypeConversion.h"

void extractString(SEXP in, std::string* out) {
Expand Down Expand Up @@ -49,7 +50,11 @@ SEXP getListElement(SEXP list, const char* str) {
}

void dump(std::vector<std::string>& s) {
#ifndef __MINGW64__
Rprintf("Dump %zu elements:\n", s.size());
#else
Rprintf("Dump %lu elements:\n", (unsigned long int)s.size());
#endif
for (unsigned int i = 0; i != s.size(); i++) {
Rprintf("s[%u] = \"%s\"\n", i, s[i].c_str());
}
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8 changes: 6 additions & 2 deletions src/RangeList.h
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Original file line number Diff line number Diff line change
Expand Up @@ -329,7 +329,11 @@ class RangeList{
std::string out;
for (size_t i = 0; i != this->size(); ++i) {
this->obtainRange(i, &out);
#ifndef __MINGW64__
REprintf( "range %zu: %s\n", i, out.c_str());
#else
REprintf( "range %lu: %s\n", (unsigned long int)i, out.c_str());
#endif
}
};
class iterator{
Expand All @@ -346,7 +350,7 @@ class RangeList{
positionPair(NULL){
chromSize = rc.getChromVector().size();
inChromRegionSize = getRegions(chromIndex)? getRegions(chromIndex)->size() : 0;
if (chromSize && chromIndex < chromSize) {
if (chromSize && chromIndex < (int) chromSize) {
chrom = &(rc.getChromVector()[chromIndex]);
positionPair = getRegions(chromIndex);
}
Expand All @@ -358,7 +362,7 @@ class RangeList{
this->inChromRangeIndex = 0;
chromSize = this->rangeCollection->getChromVector().size();
inChromRegionSize = getRegions(chromIndex)? getRegions(chromIndex)->size() : 0;
chrom = chromIndex < chromSize ? &(this->rangeCollection->getChromVector()[chromIndex]) : NULL;
chrom = chromIndex < (int) chromSize ? &(this->rangeCollection->getChromVector()[chromIndex]) : NULL;
positionPair = getRegions(chromIndex);
}
return (*this);
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133 changes: 85 additions & 48 deletions src/SingleChromosomeBCFIndex.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,9 @@ struct Record {
bool operator<(Record& o) { return (pos < o.pos); }
};

static bool comparator(const Record& a, const Record& b) { return a.pos < b.pos; }
static bool comparator(const Record& a, const Record& b) {
return a.pos < b.pos;
}

SingleChromosomeBCFIndex::SingleChromosomeBCFIndex(
const std::string& bcfFile, const std::string& indexFile) {
Expand All @@ -41,7 +43,7 @@ void SingleChromosomeBCFIndex::close() {

void SingleChromosomeBCFIndex::closeIndex() {
if (data_) {
delete[](uint8_t*) data_;
delete[] (uint8_t*)data_;
data_ = NULL;
}
}
Expand All @@ -62,65 +64,75 @@ int SingleChromosomeBCFIndex::createIndex() {
// check magic number
char magic[5];
if (5 != bgzf_read(fp, magic, 5)) {
return -1; // exit(1);
return -1; // exit(1);
}
if (!(magic[0] == 'B' && magic[1] == 'C' && magic[2] == 'F' &&
magic[3] == 2 && (magic[4] == 1 || magic[4] == 2))) {
return -1; // exit(1);
return -1; // exit(1);
}

// read header
uint32_t l_text;
if (4 != bgzf_read(fp, &l_text, 4)) {
return -1; // exit(1);
return -1; // exit(1);
}
Rprintf("l_text = %d\n", l_text);

std::string s;
int64_t bgzf_offset_before_header = bgzf_tell(fp); // the beginning of header block
int64_t bgzf_offset_before_header =
bgzf_tell(fp); // the beginning of header block
s.resize(l_text);
if (bgzf_read(fp, (void*)s.data(), l_text) != l_text) {
REprintf( "Read failed!\n");
REprintf("Read failed!\n");
}
BCFHeader bcfHeader;
if (bcfHeader.parseHeader(s,
&bcfHeader.header_contig_id,
&bcfHeader.header_id,
&bcfHeader.header_number,
&bcfHeader.header_type,
&bcfHeader.header_description)) {
REprintf( "Parse header failed!\n");
return -1; // exit(1);
if (bcfHeader.parseHeader(s, &bcfHeader.header_contig_id,
&bcfHeader.header_id, &bcfHeader.header_number,
&bcfHeader.header_type,
&bcfHeader.header_description)) {
REprintf("Parse header failed!\n");
return -1; // exit(1);
}

// locate #CHROM line
int64_t bgzf_offset_after_header = bgzf_tell(fp); // the end of header block
size_t ptr_chrom_line = s.find("#CHROM"); // the index of "#CHROM", also the size between beginning of header to '#CHROM'
int64_t bgzf_offset_after_header = bgzf_tell(fp); // the end of header block
size_t ptr_chrom_line =
s.find("#CHROM"); // the index of "#CHROM", also the size between
// beginning of header to '#CHROM'
if (ptr_chrom_line == std::string::npos) {
REprintf( "Cannot find the \"#CHROM\" line!\n");
return -1; // exit(1);
REprintf("Cannot find the \"#CHROM\" line!\n");
return -1; // exit(1);
}
Rprintf("offset_header = %d\n", (int) ptr_chrom_line);
Rprintf("offset_header = %d\n", (int)ptr_chrom_line);

bgzf_seek(fp, bgzf_offset_before_header, SEEK_SET); // rewind fp to the beginning of header
bgzf_seek(fp, bgzf_offset_before_header,
SEEK_SET); // rewind fp to the beginning of header
s.resize(ptr_chrom_line);
int64_t before_chrom_size = bgzf_read(fp, (void*) s.data(), ptr_chrom_line);
int64_t bgzf_offset_before_chrom = bgzf_tell(fp); // the offset to #CHROM
int64_t before_chrom_size = bgzf_read(fp, (void*)s.data(), ptr_chrom_line);
int64_t bgzf_offset_before_chrom = bgzf_tell(fp); // the offset to #CHROM
s.resize(l_text - before_chrom_size);
int64_t after_chrom_size = bgzf_read(fp, (void*) s.data(), l_text - before_chrom_size);
int64_t after_chrom_size =
bgzf_read(fp, (void*)s.data(), l_text - before_chrom_size);
int32_t last_character = s[after_chrom_size - 1];
// load sample names
while (s.back() == '\n' || s.back() == '\0') {
s.resize(s.size() - 1);
}
stringTokenize(s, "\t", &bcfHeader.sample_names);
const int64_t num_sample = (int)bcfHeader.sample_names.size() - 9; // vcf header has 9 columns CHROM...FORMAT before actual sample names
const int64_t num_sample =
(int)bcfHeader.sample_names.size() -
9; // vcf header has 9 columns CHROM...FORMAT before actual sample names
#ifndef __MINGW64__
Rprintf("sample size = %ld\n", num_sample);
Rprintf("last character is s[after_chrom_size-1] = %d\n", last_character); // should be 0, the null terminator character
#else
Rprintf("sample size = %ld\n", (unsigned long int)num_sample);
#endif
Rprintf("last character is s[after_chrom_size-1] = %d\n",
last_character); // should be 0, the null terminator character
// quality check
if (bgzf_offset_after_header != bgzf_tell(fp)) {
REprintf( "Messed up bgzf header\n");
return -1; // exit(1);
REprintf("Messed up bgzf header\n");
return -1; // exit(1);
}

// create index file
Expand All @@ -139,33 +151,43 @@ int SingleChromosomeBCFIndex::createIndex() {
do {
offset = bgzf_tell(fp);
if (4 != bgzf_read(fp, &l_shared, sizeof(uint32_t))) {
break; // REprintf( "Wrong read!\n"); exit(1);
break; // REprintf( "Wrong read!\n"); exit(1);
}
if (4 != bgzf_read(fp, &l_indiv, sizeof(uint32_t))) {
break; // REprintf( "Wrong read!\n"); exit(1);
break; // REprintf( "Wrong read!\n"); exit(1);
}
data.resize(l_shared + l_indiv);
if (l_shared + l_indiv != bgzf_read(fp, data.data(), (l_shared+l_indiv) * sizeof(char))) {
break; // REprintf( "Wrong read!\n"); exit(1);
if (l_shared + l_indiv !=
bgzf_read(fp, data.data(), (l_shared + l_indiv) * sizeof(char))) {
break; // REprintf( "Wrong read!\n"); exit(1);
}
memcpy(&pos, data.data() + 4, 4);
fwrite(&pos, sizeof(int64_t), 1, fIndex);
fwrite(&offset, sizeof(int64_t), 1, fIndex);

num_marker++;
if (num_marker % 10000 == 0) {
#ifndef __MINGW64__
Rprintf("\rprocessed %ld markers", num_marker);
#else
Rprintf("\rprocessed %ld markers", (unsigned long int)num_marker);
#endif
}
} while (true);

if (fseek(fIndex, 0, SEEK_SET)) {
REprintf( "fseek failed\n!");
REprintf("fseek failed\n!");
}
fwrite(&num_sample, sizeof(int64_t), 1, fIndex);
fwrite(&num_marker, sizeof(int64_t), 1, fIndex);
fclose(fIndex);
Rprintf("Indexing finished with %ld samples and %ld markers\n", num_sample, num_marker);

#ifndef __MINGW64__
Rprintf("Indexing finished with %ld samples and %ld markers\n", num_sample,
num_marker);
#else
Rprintf("Indexing finished with %ld samples and %ld markers\n",
(unsigned long int)num_sample, (unsigned long int)num_marker);
#endif
return 0;
}

Expand All @@ -180,12 +202,19 @@ int SingleChromosomeBCFIndex::openIndex() {
REprintf("Read incomplete index\n");
return -1;
}

// verify file integrity
int64_t* d = (int64_t*) data_;
if (fsize != sizeof(Record) * (2L + d[1])) { // d[0, 1]: number of sample; number of marker
int64_t* d = (int64_t*)data_;
if (fsize !=
sizeof(Record) *
(2L + d[1])) { // d[0, 1]: number of sample; number of marker
REprintf("Check file integrity!\n");
#ifndef __MINGW64__
REprintf("d = %ld %ld fsize = %ld\n", d[0], d[1], (long int)fsize);
#else
REprintf("d = %ld %ld fsize = %ld\n", (unsigned long int)d[0],
(unsigned long int)d[1], (long int)fsize);
#endif
return -1;
}
return 0;
Expand All @@ -209,7 +238,7 @@ int SingleChromosomeBCFIndex::query(int chromPosBeg, int chromPosEnd,

Record* r = (Record*)data_;
const int64_t Nrecord = r[0].offset;

++r; // skip the first block, as first block is (#sample, #marker)

// binary search for file position
Expand All @@ -226,7 +255,12 @@ int SingleChromosomeBCFIndex::query(int chromPosBeg, int chromPosEnd,
comparator); // r[ub].pos > query.pos = chromPosEnd
REprintf("Found %d results\n", (int)(ub - lb));
for (Record* pi = lb; pi != ub; ++pi) {
#ifndef __MINGW64__
REprintf("%ld %ld\n", pi->pos, pi->offset);
#else
REprintf("%ld %ld\n", (unsigned long int)pi->pos,
(unsigned long int)pi->offset);
#endif
// REprintf("%ld %ld\n", ub->pos, ub->offset);
*voffset = lb->offset;
break;
Expand All @@ -235,43 +269,46 @@ int SingleChromosomeBCFIndex::query(int chromPosBeg, int chromPosEnd,
REprintf("Cannot find position!\n");
return -1;
} else {
#ifndef __MINGW64__
REprintf("found %d position, e.g. %ld %ld\n", (int)(ub - lb), (*lb).pos,
(*lb).offset);
#else
REprintf("found %d position, e.g. %ld %ld\n", (int)(ub - lb),
(unsigned long int)(*lb).pos, (unsigned long int)(*lb).offset);
#endif
return ub - lb;
}
}

int SingleChromosomeBCFIndex::readLine(int64_t offset,
uint32_t* l_shared,
int SingleChromosomeBCFIndex::readLine(int64_t offset, uint32_t* l_shared,
uint32_t* l_indiv,
std::vector<char>* line) {
if (bgzf_seek(fBcfFile_, offset, SEEK_SET)) {
REprintf("seek error!\n");
}

if (4 != bgzf_read(fBcfFile_, l_shared, sizeof(uint32_t)) ||
4 != bgzf_read(fBcfFile_, l_indiv, sizeof(uint32_t))) {
REprintf("readLine error!\n");
}
uint32_t totalLen = *l_shared + *l_indiv;
uint32_t totalLen = *l_shared + *l_indiv;
line->resize(totalLen);
if ( totalLen != bgzf_read(fBcfFile_, line->data(), totalLen)) {
if (totalLen != bgzf_read(fBcfFile_, line->data(), totalLen)) {
REprintf("readLine bgzf_read error!\n");
}

return totalLen;
}

int SingleChromosomeBCFIndex::nextLine(uint32_t* l_shared,
uint32_t* l_indiv,
int SingleChromosomeBCFIndex::nextLine(uint32_t* l_shared, uint32_t* l_indiv,
std::vector<char>* line) {
if (4 != bgzf_read(fBcfFile_, l_shared, sizeof(uint32_t)) ||
4 != bgzf_read(fBcfFile_, l_indiv, sizeof(uint32_t))) {
REprintf("readLine error!\n");
}
uint32_t totalLen = *l_shared + *l_indiv;
uint32_t totalLen = *l_shared + *l_indiv;
line->resize(totalLen);
if ( totalLen != bgzf_read(fBcfFile_, line->data(), totalLen)) {
if (totalLen != bgzf_read(fBcfFile_, line->data(), totalLen)) {
REprintf("readLine bgzf_read error!\n");
}

Expand Down
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