[med-svn] [Git][med-team/libtabixpp][master] 3 commits: New upstream version 1.1.0
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Dec 14 14:30:38 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / libtabixpp
Commits:
4b17a10f by Michael R. Crusoe at 2019-12-14T14:04:32Z
New upstream version 1.1.0
- - - - -
7c8c641d by Michael R. Crusoe at 2019-12-14T14:04:34Z
Update upstream source from tag 'upstream/1.1.0'
Update to upstream version '1.1.0'
with Debian dir ae89409b8a19befd41bf1d021ac04c56b1a664e5
- - - - -
534f433a by Michael R. Crusoe at 2019-12-14T14:29:33Z
1.1.0-1
- - - - -
9 changed files:
- Makefile
- debian/changelog
- debian/control
- debian/libtabixpp0.symbols
- debian/patches/build_shared_lib_with_debian_htslib.patch
- − debian/patches/hardening
- debian/patches/series
- tabix.cpp
- tabix.hpp
Changes:
=====================================
Makefile
=====================================
@@ -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 \
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+libtabixpp (1.1.0-1) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * New upstream release.
+ * Freshen patches; hardening patch applied upstream
+ PENDING: libhts 1.10-2 with libhts3
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 14 Dec 2019 15:04:39 +0100
+
libtabixpp (1.0.0-5) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -7,6 +7,7 @@ Priority: optional
Build-Depends: debhelper (>= 11~),
libhts-dev,
zlib1g-dev,
+ libbz2-dev,
d-shlibs
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/libtabixpp
=====================================
debian/libtabixpp0.symbols
=====================================
@@ -1,5 +1,7 @@
libtabixpp.so.0 libtabixpp0 #MINVER#
_ZN5Tabix11getNextLineERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 1.0.0
+ _ZN5Tabix13getKstringPtrEv at Base 1.1.0
+ _ZN5Tabix13getNextLineKSEv at Base 1.1.0
_ZN5Tabix9getHeaderERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 1.0.0
_ZN5Tabix9setRegionERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 1.0.0
_ZN5TabixC1ERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 1.0.0
=====================================
debian/patches/build_shared_lib_with_debian_htslib.patch
=====================================
@@ -4,25 +4,28 @@ Description: Build shared lib with Debian's htslib
Debian's shared libhts from the archive.
Also builds a shared library instead of a static one.
Author: Sascha Steinbiss <sascha at steinbiss.name>
---- a/Makefile
-+++ b/Makefile
-@@ -3,11 +3,12 @@
+--- libtabixpp.orig/Makefile
++++ libtabixpp/Makefile
+@@ -3,7 +3,7 @@
CC?= gcc
CXX?= g++
-CXXFLAGS?= -g -Wall -O2 -fPIC #-m64 #-arch ppc
-+CXXFLAGS+= -fPIC
++CXXFLAGS+= -fPIC
INCLUDES?= -Ihtslib
HTS_HEADERS?= htslib/htslib/bgzf.h htslib/htslib/tbx.h
HTS_LIB?= htslib/libhts.a
- LIBPATH?= -L. -Lhtslib
-+SONUMBER=0
-
+@@ -12,6 +12,7 @@
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
PROG= tabix++
-@@ -18,32 +19,24 @@
+ SUBDIRS=.
++SONUMBER=0
+
+ ifeq ($(OS),Windows_NT)
+ LIBS += -lws2_32
+@@ -22,31 +23,22 @@
.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//`; \
@@ -34,13 +37,13 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
- || exit 1; \
- cd $$wdir; \
- done;
-+all: $(PROG) libtabixpp.so.$(SONUMBER) libtabixpp.a
++all: $(PROG) libtabixpp.so.$(SONUMBER) libtabixpp.a
-all: $(PROG)
-
-tabix.o: $(HTS_HEADERS) tabix.cpp tabix.hpp
+tabix.o: 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
@@ -52,15 +55,13 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
-tabix++: tabix.o main.cpp $(HTS_LIB)
+tabix++: tabix.o main.cpp
- $(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.pdf *.class libtabix.*.dylib libtabix.so*
- cd htslib && $(MAKE) clean
+ tabix.pdf *.class libtabix*.dylib libtabix*so*
-+ #cd htslib && $(MAKE) clean
-clean:cleanlocal-recur
+clean: cleanlocal
=====================================
debian/patches/hardening deleted
=====================================
@@ -1,28 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: enable hardening flags passthrough
---- libtabixpp.orig/Makefile
-+++ libtabixpp/Makefile
-@@ -17,12 +17,12 @@
- .SUFFIXES:.c .o
-
- .c.o:
-- $(CC) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-+ $(CC) $(CPPFLAGS) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-
- all: $(PROG) libtabixpp.so.$(SONUMBER) libtabixpp.a
-
- tabix.o: tabix.cpp tabix.hpp
-- $(CXX) $(CXXFLAGS) -c tabix.cpp $(INCLUDES)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -c tabix.cpp $(INCLUDES)
-
- libtabixpp.a: tabix.o
- ar rcs $@ $<
-@@ -31,7 +31,7 @@
- $(CXX) -shared -o $@ $< -fPIC -Wl,-soname,libtabixpp.so.$(SONUMBER) $(LDFLAGS) -lhts
-
- tabix++: tabix.o main.cpp
-- $(CXX) $(CXXFLAGS) -o $@ main.cpp tabix.o $(INCLUDES) $(LIBPATH) \
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $@ main.cpp tabix.o $(INCLUDES) $(LIBPATH) \
- -lhts -lpthread -lm -lz
-
- cleanlocal:
=====================================
debian/patches/series
=====================================
@@ -1,2 +1 @@
build_shared_lib_with_debian_htslib.patch
-hardening
=====================================
tabix.cpp
=====================================
@@ -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
=====================================
@@ -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();
};
View it on GitLab: https://salsa.debian.org/med-team/libtabixpp/compare/6f269a28e008a608320f8346f05da5cc5c101fc4...534f433aebb094d457f01e9bcb03a1a28c365a30
--
View it on GitLab: https://salsa.debian.org/med-team/libtabixpp/compare/6f269a28e008a608320f8346f05da5cc5c101fc4...534f433aebb094d457f01e9bcb03a1a28c365a30
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