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Author: Dylan Aïssi <bob.dybian@gmail.com>
Description: Merge src/utils/tabix.*pp with upstream (libtabixpp 1.0.0) in order to use libhts instead libtabix.
Last-Update: 2016-04-29
Forwarded: no
--- a/Makefile
+++ b/Makefile
@@ -52,7 +52,7 @@
LIB_TABX=$(PATH_TABX)/libtabix.a
else
LIB_MATH=-lRmath
- LIB_TABX=-ltabix
+ LIB_TABX=-lhts
endif
LIB_MACX=-L/usr/local/lib/
--- a/src/utils/tabix.cpp
+++ b/src/utils/tabix.cpp
@@ -8,6 +8,7 @@
Tabix::Tabix(void) { }
Tabix::Tabix(string& file) {
+ has_jumped = false;
filename = file;
const char* cfilename = file.c_str();
struct stat stat_tbi,stat_vcf;
@@ -30,78 +31,99 @@
}
free(fnidx);
- if ((t = ti_open(cfilename, 0)) == 0) {
+ if ((fn = hts_open(cfilename, "r")) == 0) {
cerr << "[tabix++] fail to open the data file." << endl;
exit(1);
}
- if (ti_lazy_index_load(t) < 0) {
+ if ((tbx = tbx_index_load(cfilename)) == NULL) {
cerr << "[tabix++] failed to load the index file." << endl;
exit(1);
}
- idxconf = ti_get_conf(t->idx);
+ 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
- iter = ti_query(t, 0, 0, 0);
+ current_chrom = chroms.begin();
+ iter = tbx_itr_querys(tbx, current_chrom->c_str());
}
Tabix::~Tabix(void) {
- ti_iter_destroy(iter);
- ti_close(t);
+ tbx_itr_destroy(iter);
+ tbx_destroy(tbx);
}
void Tabix::getHeader(string& header) {
header.clear();
- ti_iter_destroy(iter);
- iter = ti_query(t, 0, 0, 0);
- const char* s;
- int len;
- while ((s = ti_read(t, iter, &len)) != 0) {
- if ((int)(*s) != idxconf->meta_char) {
- firstline = string(s); // stash this line
+ kstring_t str = {0,0,0};
+ while ( hts_getline(fn, KS_SEP_LINE, &str) >= 0 ) {
+ if ( !str.l || str.s[0]!=tbx->conf.meta_char ) {
break;
} else {
- header += string(s);
+ 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->c_str());
}
void Tabix::getLastHeader(string & header) {
- header.clear();
- ti_iter_destroy(iter);
- iter = ti_query(t, 0, 0, 0);
- const char* s;
- int len;
- while ((s = ti_read(t, iter, &len)) != 0) {
- if ((int)(*s) != idxconf->meta_char) {
- firstline = string(s); // stash this line
- break;
- } else header = string(s);
- }
+ header.clear();
+ kstring_t str = {0,0,0};
+ 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);
+ }
+ // set back to start
+ current_chrom = chroms.begin();
+ if (iter) tbx_itr_destroy(iter);
+ iter = tbx_itr_querys(tbx, current_chrom->c_str());
}
bool Tabix::setRegion(string region) {
- if (ti_parse_region(t->idx, region.c_str(), &tid, &beg, &end) == 0) {
- firstline.clear();
- ti_iter_destroy(iter);
- iter = ti_queryi(t, tid, beg, end);
- return true;
- } else return false;
+ tbx_itr_destroy(iter);
+ iter = tbx_itr_querys(tbx, region.c_str());
+ has_jumped = true;
+ return true;
}
bool Tabix::getNextLine(string & line) {
- const char* s;
- int len;
- if (!firstline.empty()) {
- line = firstline; // recovers line read if header is parsed
- firstline.clear();
- return true;
- }
- if ((s = ti_read(t, iter, &len)) != 0) {
- line = string(s);
- return true;
- } else return false;
+ kstring_t str = {0,0,0};
+ 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 {
+ ++current_chrom;
+ while (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;
+ }
+ }
}
--- a/src/utils/tabix.hpp
+++ b/src/utils/tabix.hpp
@@ -9,24 +9,31 @@
#include <string>
#include <stdlib.h>
#include <sys/stat.h>
-#include <bgzf.h>
-#include <tabix.h>
+#include <htslib/bgzf.h>
+#include <htslib/tbx.h>
+#include <htslib/kseq.h>
#include <iostream>
+#include <cstring>
+#include <vector>
using namespace std;
class Tabix {
- tabix_t *t;
- ti_iter_t iter;
- const ti_conf_t *idxconf;
+ htsFile* fn;
+ tbx_t* tbx;
+ hts_itr_t* iter;
+ const tbx_conf_t *idxconf;
int tid, beg, end;
string firstline;
+ bool has_jumped;
+ vector<string>::iterator current_chrom;
public:
string filename;
+ vector<string> chroms;
Tabix(void);
Tabix(string& file);
@@ -36,6 +43,7 @@
void getLastHeader(string & header);
bool setRegion(string region);
bool getNextLine(string& line);
+
};
#endif
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