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#include "tabix.hpp"
Tabix::Tabix(void) { }
Tabix::Tabix(string& file) {
has_jumped = false;
filename = file;
str.l = 0;
str.m = 0;
str.s = NULL;
const char* cfilename = file.c_str();
struct stat stat_tbi,stat_vcf;
char *fnidx = (char*) calloc(strlen(cfilename) + 5, 1);
strcat(strcpy(fnidx, cfilename), ".tbi");
if ( bgzf_is_bgzf(cfilename)!=1 )
{
cerr << "[tabix++] was bgzip used to compress this file? " << file << endl;
free(fnidx);
exit(1);
}
// Common source of errors: new VCF is used with an old index
stat(fnidx, &stat_tbi);
stat(cfilename, &stat_vcf);
if ( stat_vcf.st_mtime > stat_tbi.st_mtime )
{
cerr << "[tabix++] the index file is older than the vcf file. Please use '-f' to overwrite or reindex." << endl;
free(fnidx);
exit(1);
}
free(fnidx);
if ((fn = hts_open(cfilename, "r")) == 0) {
cerr << "[tabix++] fail to open the data file." << endl;
exit(1);
}
if ((tbx = tbx_index_load(cfilename)) == NULL) {
cerr << "[tabix++] failed to load the index file." << endl;
exit(1);
}
int nseq;
const char** seq = tbx_seqnames(tbx, &nseq);
for (int i=0; i<nseq; i++) {
chroms.push_back(seq[i]);
}
free(seq);
idxconf = &tbx_conf_vcf;
// set up the iterator, defaults to the beginning
current_chrom = chroms.begin();
iter = tbx_itr_querys(tbx, (current_chrom != chroms.end() ? current_chrom->c_str() : ""));
}
Tabix::~Tabix(void) {
tbx_itr_destroy(iter);
tbx_destroy(tbx);
free(str.s);
}
const kstring_t * Tabix::getKstringPtr(){
return &str;
}
void Tabix::getHeader(string& header) {
header.clear();
while ( hts_getline(fn, KS_SEP_LINE, &str) >= 0 ) {
if ( !str.l || str.s[0]!=tbx->conf.meta_char ) {
break;
} else {
header += string(str.s);
header += "\n";
}
}
// set back to start
current_chrom = chroms.begin();
if (iter) tbx_itr_destroy(iter);
iter = tbx_itr_querys(tbx, (current_chrom != chroms.end() ? current_chrom->c_str() : ""));
}
bool Tabix::setRegion(string& region) {
tbx_itr_destroy(iter);
iter = tbx_itr_querys(tbx, region.c_str());
has_jumped = true;
return true;
}
bool Tabix::getNextLine(string& line) {
if (has_jumped) {
if (iter && tbx_itr_next(fn, tbx, iter, &str) >= 0) {
line = string(str.s);
return true;
} else return false;
} else { // step through all sequences in the file
// we've never jumped, so read everything
if (iter && tbx_itr_next(fn, tbx, iter, &str) >= 0) {
line = string(str.s);
return true;
} else {
// While we aren't at the end, advance. While we're still not at the end...
while (current_chrom != chroms.end() && ++current_chrom != chroms.end()) {
tbx_itr_destroy(iter);
iter = tbx_itr_querys(tbx, current_chrom->c_str());
if (iter && tbx_itr_next(fn, tbx, iter, &str) >= 0) {
line = string(str.s);
return true;
} else {
++current_chrom;
}
}
return false;
}
}
}
bool Tabix::getNextLineKS() {
if (has_jumped) {
if (iter &&
tbx_itr_next(fn, tbx, iter, &str) >= 0) {
//line = &str;
return true;
} else
return false;
} else { // step through all sequences in the file
// we've never jumped, so read everything
if (iter && tbx_itr_next(fn, tbx, iter, &str) >= 0) {
//line = &str;
return true;
} else {
// While we aren't at the end, advance. While we're still not at the end...
while (current_chrom != chroms.end() && ++current_chrom != chroms.end()) {
tbx_itr_destroy(iter);
iter = tbx_itr_querys(tbx, current_chrom->c_str());
if (iter && tbx_itr_next(fn, tbx, iter, &str) >= 0) {
//line = &str;
return true;
} else {
++current_chrom;
}
}
return false;
}
}
}
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