Commit 4b17a10f authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 1.1.0

parent f9c33b4e

Makefile

+8 −5
Original line number Diff line number Diff line
@@ -8,15 +8,19 @@ INCLUDES?= -Ihtslib 
HTS_HEADERS?=	htslib/htslib/bgzf.h htslib/htslib/tbx.h

HTS_LIB?=	htslib/libhts.a

LIBPATH?=	-L. -Lhtslib



LIBS?=	-lhts -lpthread -lm -lbz2 -llzma -lz

DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE

PROG=		tabix++

SUBDIRS=.



ifeq ($(OS),Windows_NT)

	LIBS += -lws2_32

endif



.SUFFIXES:.c .o



.c.o:

	$(CC) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@

	$(CC) $(CPPFLAGS) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@



all-recur lib-recur clean-recur cleanlocal-recur install-recur:

	@target=`echo $@ | sed s/-recur//`; \
@@ -32,14 +36,13 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur: 
all:	$(PROG)



tabix.o: $(HTS_HEADERS) tabix.cpp tabix.hpp

	$(CXX) $(CXXFLAGS) -c tabix.cpp $(INCLUDES)

	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c tabix.cpp $(INCLUDES)



htslib/libhts.a:

	cd htslib && $(MAKE) lib-static



tabix++: tabix.o main.cpp $(HTS_LIB)

	$(CXX) $(CXXFLAGS) -o $@ main.cpp tabix.o $(INCLUDES) $(LIBPATH) \

		-lhts -lpthread -lm -lz

	$(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $@ main.cpp tabix.o $(INCLUDES) $(LIBPATH) $(LIBS)



cleanlocal:

	rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log \

tabix.cpp

+42 −6
Original line number Diff line number Diff line
@@ -5,6 +5,9 @@ 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);
@@ -47,18 +50,22 @@ Tabix::Tabix(string& file) { 


    // set up the iterator, defaults to the beginning

    current_chrom = chroms.begin();

    iter = tbx_itr_querys(tbx, current_chrom->c_str());

    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();

    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;
@@ -70,7 +77,7 @@ void Tabix::getHeader(string& header) { 
    // set back to start

    current_chrom = chroms.begin();

    if (iter) tbx_itr_destroy(iter);

    iter = tbx_itr_querys(tbx, current_chrom->c_str());

    iter = tbx_itr_querys(tbx, (current_chrom != chroms.end() ? current_chrom->c_str() : ""));

}



bool Tabix::setRegion(string& region) {
@@ -81,7 +88,6 @@ bool Tabix::setRegion(string& region) { 
}



bool Tabix::getNextLine(string& line) {

    kstring_t str = {0,0,0};

    if (has_jumped) {

        if (iter && tbx_itr_next(fn, tbx, iter, &str) >= 0) {

            line = string(str.s);
@@ -93,8 +99,8 @@ bool Tabix::getNextLine(string& line) { 
            line = string(str.s);

            return true;

        } else {

            ++current_chrom;

            while (current_chrom != chroms.end()) {

            // 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) {
@@ -108,3 +114,33 @@ bool Tabix::getNextLine(string& line) { 
        }

    }

}



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;

        }

    }

}

tabix.hpp

+3 −1
Original line number Diff line number Diff line
@@ -15,6 +15,7 @@ class Tabix { 


    htsFile* fn;

    tbx_t* tbx;

    kstring_t str;

    hts_itr_t* iter;

    const tbx_conf_t *idxconf;

    int tid, beg, end;
@@ -23,7 +24,6 @@ class Tabix { 
    vector<string>::iterator current_chrom;



public:



    string filename;

    vector<string> chroms;
@@ -31,8 +31,10 @@ public: 
    Tabix(string& file);

    ~Tabix(void);



    const kstring_t * getKstringPtr();

    void getHeader(string& header);

    bool setRegion(string& region);

    bool getNextLine(string& line);

    bool getNextLineKS();



};