[med-svn] [Git][med-team/libmaus2][master] 5 commits: New upstream version 2.0.719+dfsg
Andreas Tille
gitlab at salsa.debian.org
Thu May 28 08:08:51 BST 2020
Andreas Tille pushed to branch master at Debian Med / libmaus2
Commits:
a4548fd8 by Andreas Tille at 2020-05-28T08:04:05+02:00
New upstream version 2.0.719+dfsg
- - - - -
b005c675 by Andreas Tille at 2020-05-28T08:04:05+02:00
routine-update: New upstream version
- - - - -
30cdbf40 by Andreas Tille at 2020-05-28T08:04:11+02:00
Update upstream source from tag 'upstream/2.0.719+dfsg'
Update to upstream version '2.0.719+dfsg'
with Debian dir c4bb22eca0b82d41516224d45249d17d79fd7de2
- - - - -
76b73915 by Andreas Tille at 2020-05-28T08:04:11+02:00
routine-update: debhelper-compat 13
- - - - -
a7bebcba by Andreas Tille at 2020-05-28T09:08:25+02:00
Upload to unstable
- - - - -
18 changed files:
- ChangeLog
- configure.ac
- debian/changelog
- debian/control
- src/Makefile.am
- src/libmaus2/LibMausConfig.hpp.in
- src/libmaus2/StaticInitialization.cpp
- src/libmaus2/avl/AVLSet.hpp
- src/libmaus2/math/binom.hpp
- src/libmaus2/parallel/SimpleThreadPool.hpp
- src/libmaus2/sorting/InPlaceParallelSort.hpp
- src/libmaus2/sorting/ParallelStableSort.hpp
- + src/libmaus2/util/StackLineTranslator.hpp
- src/libmaus2/util/StackTrace.cpp
- + src/libmaus2/util/StackTraceBufferContainer.cpp
- + src/libmaus2/util/StackTraceBufferContainer.hpp
- src/libmaus2/util/TabEntry.hpp
- src/libmaus2/vcf/VCFParser.hpp
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,43 @@
+libmaus2 (2.0.719-1) unstable; urgency=medium
+
+ * Make separator in VCFParser::getSampleValueVectorForKey a template argument
+ * Add comments in InPlaceParallelSort
+ * Add comment describing binomRowUpper in Binom class
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Thu, 14 May 2020 10:36:05 +0200
+
+libmaus2 (2.0.718-1) unstable; urgency=medium
+
+ * Add runFilterFilterFlags in VCFParser
+ * Avoid using operator!= on value_type in AVLSet
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Thu, 07 May 2020 13:23:27 +0200
+
+libmaus2 (2.0.717-1) unstable; urgency=medium
+
+ * move loop end computation before loop in ParallelStableSort
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Fri, 17 Apr 2020 20:27:39 +0200
+
+libmaus2 (2.0.716-1) unstable; urgency=medium
+
+ * Add getUnquoted* methods in TabEntry
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Fri, 17 Apr 2020 14:01:23 +0200
+
+libmaus2 (2.0.715-1) unstable; urgency=medium
+
+ * refactor
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Thu, 02 Apr 2020 10:09:56 +0200
+
+libmaus2 (2.0.714-1) unstable; urgency=medium
+
+ * Make segfault handler controllable by environment variables LIBMAUS2_TRACE_SEGFAULT/LIBMAUS2_TRACE_SEGFAULT_TRANSLATE
+ * Add StackTraceBufferContainer for obtaining stack traces from segmentation faults
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Fri, 27 Mar 2020 14:22:47 +0100
+
libmaus2 (2.0.713-1) unstable; urgency=medium
* Add new interface for setting CRAM compression profile in parallel CRAM encoding
=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
-AC_INIT(libmaus2,2.0.713,[germant at miltnyibiotec.de],[libmaus2],[https://github.com/gt1/libmaus2])
-LIBRARY_VERSION=2:713:0
+AC_INIT(libmaus2,2.0.719,[germant at miltnyibiotec.de],[libmaus2],[https://github.com/gt1/libmaus2])
+LIBRARY_VERSION=2:719:0
AC_MSG_NOTICE([Configuring for source in directory ${srcdir}])
AC_CANONICAL_SYSTEM
AC_CANONICAL_HOST
@@ -110,8 +110,16 @@ AC_CHECK_HEADER(features.h, [LIBMAUS2_HAVE_FEATURES_H="#define LIBMAUS2_HAVE_FEA
AC_CHECK_HEADER(stdint.h, [LIBMAUS2_HAVE_STDINT_H="#define LIBMAUS2_HAVE_STDINT_H"], [LIBMAUS2_HAVE_STDINT_H=])
AC_CHECK_HEADER(dlfcn.h, [LIBMAUS2_HAVE_DLFCN_H="#define LIBMAUS2_HAVE_DLFCN_H"], [LIBMAUS2_HAVE_DLFCN_H=])
AC_CHECK_HEADER(sys/prctl.h, [LIBMAUS2_HAVE_SYS_PRCTL_H="#define LIBMAUS2_HAVE_SYS_PRCTL_H"], [LIBMAUS2_HAVE_SYS_PRCTL_H=])
+AC_CHECK_HEADER(libunwind.h, [LIBMAUS2_HAVE_LIBUNWIND_H="#define LIBMAUS2_HAVE_LIBUNWIND_H"], [LIBMAUS2_HAVE_LIBUNWIND_H=])
AC_LANG_POP
+AC_CHECK_LIB([unwind],[unw_backtrace],[unw_backtrace=yes],[unw_backtrace=no])
+
+LIBMAUS2_HAVE_UNW_BACKTRACE=
+if test "${unw_backtrace}" = "yes" ; then
+ LIBMAUS2_HAVE_UNW_BACKTRACE="#define LIBMAUS2_HAVE_UNW_BACKTRACE"
+fi
+
LIBMAUSCPPFLAGS="${CPPFLAGS}"
LIBMAUSLDFLAGS="${LDFLAGS}"
@@ -410,6 +418,10 @@ fi
LIBMAUSLIBS="${LIBMAUSLIBS} ${ZLIBLIBS}"
+if test "${unw_backtrace}" = "yes" ; then
+ LIBMAUSLIBS="${LIBMAUSLIBS} -lunwind"
+fi
+
AC_LANG_PUSH([C++])
AC_MSG_CHECKING([whether SIGPIPE exists])
AC_TRY_COMPILE([#include <csignal>
@@ -3307,4 +3319,6 @@ AC_SUBST([LIBMAUS2_HAVE_IO_LIB_CRAM_ENCODER_GET_FD])
AC_SUBST([LIBMAUS2_HAVE_IO_LIB_BAMBAM_H])
AC_SUBST([LIBMAUS2_HAVE_IO_LIB_CRAM_SET_OPTION])
AC_SUBST([LIBMAUS2_IO_LIB_HAVE_CRAM_OPT_PROFILE])
+AC_SUBST([LIBMAUS2_HAVE_LIBUNWIND_H])
+AC_SUBST([LIBMAUS2_HAVE_UNW_BACKTRACE])
AC_OUTPUT(Makefile src/Makefile libmaus2.pc libmaus2irods.pc ubuntu.sh src/libmaus2/LibMausConfig.hpp test/Makefile)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+libmaus2 (2.0.719+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * debhelper-compat 13 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Thu, 28 May 2020 08:04:21 +0200
+
libmaus2 (2.0.713+ds-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>,
Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
d-shlibs,
pkg-config,
zlib1g-dev
=====================================
src/Makefile.am
=====================================
@@ -227,7 +227,8 @@ libmaus2_la_SOURCES = libmaus2/StaticInitialization.cpp \
libmaus2/bambam/ChecksumsFactory.cpp \
libmaus2/vcf/VCFSortEntry.cpp \
libmaus2/parallel/StdMutex.cpp \
- libmaus2/parallel/StdSpinLock.cpp
+ libmaus2/parallel/StdSpinLock.cpp \
+ libmaus2/util/StackTraceBufferContainer.cpp
noinst_HEADERS = libmaus2/lz/lz4.h
@@ -1329,7 +1330,9 @@ libmaus2util_include_HEADERS=\
libmaus2/util/AutoArrayUInt8TBaseAllocator.hpp \
libmaus2/util/AutoArrayUInt8TBaseTypeInfo.hpp \
libmaus2/util/DirectoryStructure.hpp \
- libmaus2/util/StreamGetObject.hpp
+ libmaus2/util/StreamGetObject.hpp \
+ libmaus2/util/StackTraceBufferContainer.hpp \
+ libmaus2/util/StackLineTranslator.hpp
libmaus2uint_includedir=$(includedir)/libmaus2/uint
libmaus2uint_include_HEADERS=\
=====================================
src/libmaus2/LibMausConfig.hpp.in
=====================================
@@ -170,3 +170,5 @@
@LIBMAUS2_HAVE_SYNC_OPS@
@LIBMAUS2_LARGEFILE_SOURCE@
@LIBMAUS2_IRODS_NEED_PREFIX@
+ at LIBMAUS2_HAVE_LIBUNWIND_H@
+ at LIBMAUS2_HAVE_UNW_BACKTRACE@
=====================================
src/libmaus2/StaticInitialization.cpp
=====================================
@@ -23,6 +23,59 @@ libmaus2::aio::StreamLock::lock_type libmaus2::aio::StreamLock::coutlock;
libmaus2::aio::StreamLock::lock_type libmaus2::aio::StreamLock::cerrlock;
libmaus2::aio::StreamLock::lock_type libmaus2::aio::StreamLock::cinlock;
+#include <libmaus2/util/StackTraceBufferContainer.hpp>
+
+libmaus2::util::StackTraceBufferContainer::id_trace_type libmaus2::util::StackTraceBufferContainer::traces[StackTraceBufferContainer_MAXTRACES];
+std::size_t volatile libmaus2::util::StackTraceBufferContainer::numtraces = 0;
+sighandler_t libmaus2::util::StackTraceBufferContainer::prevsig = nullptr;
+jmp_buf libmaus2::util::StackTraceBufferContainer::segenv;
+
+#include <unistd.h>
+
+static int parseVal(char const * p)
+{
+ unsigned int v = 0;
+
+ while ( *p )
+ {
+ if ( *p < '0' || *p > '9' )
+ return -1;
+ else
+ {
+ v *= 10;
+ v += *p-'0';
+ p++;
+ }
+ }
+ return v;
+}
+
+static int initStackTraceBufferContainer()
+{
+ char const * checkseg = getenv("LIBMAUS2_TRACE_SEGFAULT");
+
+ if ( checkseg && parseVal(checkseg) > 0 )
+ {
+ std::cerr << "[V] running libmaus2::util::StackTraceBufferContainer::setup()" << std::endl;
+ return libmaus2::util::StackTraceBufferContainer::setup();
+ }
+ else
+ return 0;
+}
+
+static int initStackTraceBufferContainerTranslate()
+{
+ char const * checkseg = getenv("LIBMAUS2_TRACE_SEGFAULT_TRANSLATE");
+
+ if ( checkseg && parseVal(checkseg) > 0 )
+ return 1;
+ else
+ return 0;
+}
+
+int libmaus2::util::StackTraceBufferContainer::init = initStackTraceBufferContainer();
+int libmaus2::util::StackTraceBufferContainer::itranslate = initStackTraceBufferContainerTranslate();
+
#include <libmaus2/types/types.hpp>
#include <libmaus2/autoarray/AutoArray.hpp>
#include <libmaus2/util/stringFunctions.hpp>
=====================================
src/libmaus2/avl/AVLSet.hpp
=====================================
@@ -755,7 +755,7 @@ namespace libmaus2
const_iterator it(this,prev);
assert ( it != end() );
- assert ( *it != v );
+ assert ( order(*it,v) || order(v,*it) );
if ( order(*it,v) )
++it;
=====================================
src/libmaus2/math/binom.hpp
=====================================
@@ -276,9 +276,14 @@ namespace libmaus2
return r;
}
+ /**
+ * return upper sum of binomial row, i.e.
+ *
+ * \sum_{i=k}^{n} binom(i,n) p^{i} (1-p)^{n-i}
+ **/
static double binomRowUpper(double const p, uint64_t const k, uint64_t const n)
{
- if ( p == 1.0 )
+ if ( p >= 1.0 )
{
if ( k <= n )
return 1;
=====================================
src/libmaus2/parallel/SimpleThreadPool.hpp
=====================================
@@ -82,7 +82,7 @@ namespace libmaus2
SimpleThreadPool(
uint64_t const rnumthreads
)
- : nextpackageid(0), panicflag(false), threads(rnumthreads), AID(rnumthreads)
+ : nextDispatcherId(0), nextpackageid(0), panicflag(false), threads(rnumthreads), AID(rnumthreads)
{
for ( uint64_t i = 0; i < threads.size(); ++i )
{
=====================================
src/libmaus2/sorting/InPlaceParallelSort.hpp
=====================================
@@ -423,7 +423,8 @@ namespace libmaus2
p+l0,
p+l0+l1,
p+l0+l1+r0,
- numthreads);
+ numthreads
+ );
// std::cerr << "l1=" << l1 << " r0=" << r0 << std::endl;
@@ -620,12 +621,15 @@ namespace libmaus2
uint64_t const numthreads
)
{
+ // size of array
uint64_t const n = e-a;
if ( ! n )
return;
+ // block size
uint64_t const s0 = (n+numthreads-1)/numthreads;
+ // number of blocks
uint64_t const b = (n+s0-1)/s0;
#if defined(_OPENMP)
@@ -638,20 +642,24 @@ namespace libmaus2
std::sort(a+low,a+high,order);
}
- // std::cerr << "sorted blocks." << std::endl;
-
+ // merge blocks
for ( uint64_t s = s0; s < n; s <<= 1 )
{
+ // number of input blocks
uint64_t const inblocks = (n+s-1)/s;
+ // output blocks
uint64_t const outblocks = (inblocks+1)>>1;
+ // iterate over output blocks
for ( uint64_t o = 0; o < outblocks; ++o )
{
+ // input ranges
uint64_t const low0 = 2*o*s;
uint64_t const high0 = std::min(low0+s,n);
uint64_t const low1 = high0;
uint64_t const high1 = std::min(low1+s,n);
+ // work request vectors
std::vector< MergeStepRecSerialRequest<iterator,order_type,base_sort> > reqvec;
int levelthres = 0;
@@ -659,7 +667,17 @@ namespace libmaus2
while ( (1ull<<levelthres) < packsperthread*numthreads )
++levelthres;
- mergestepRecLevel(a+low0,high0-low0,high1-low1,order,basesort,0,levelthres,reqvec,numthreads);
+ mergestepRecLevel(
+ a+low0,
+ high0-low0,
+ high1-low1,
+ order,
+ basesort,
+ 0,
+ levelthres,
+ reqvec,
+ numthreads
+ );
// std::cerr << "Calling dispatch for " << reqvec.size() << std::endl;
=====================================
src/libmaus2/sorting/ParallelStableSort.hpp
=====================================
@@ -304,11 +304,13 @@ namespace libmaus2
**/
void subdispatch()
{
+ int64_t const loopend = static_cast<int64_t>(mergeRequests.size());
+
#if defined(_OPENMP)
unsigned int const num_threads = context.num_threads;
#pragma omp parallel for num_threads(num_threads)
#endif
- for ( int64_t t = 0; t < static_cast<int64_t>(mergeRequests.size()); ++t )
+ for ( int64_t t = 0; t < loopend; ++t )
mergeRequests[t].dispatch();
}
};
@@ -344,7 +346,7 @@ namespace libmaus2
void dispatch()
{
- for ( level_type * cur = levels.size() ? &levels[0] : 0; cur; cur = cur->next )
+ for ( level_type * cur = levels.size() ? &levels[0] : nullptr; cur; cur = cur->next )
{
cur->dispatch();
cur->subdispatch();
@@ -408,11 +410,13 @@ namespace libmaus2
void dispatch()
{
+ int64_t const lnumpacks = static_cast<int64_t>(context->numpacks);
+
#if defined(_OPENMP)
unsigned int const num_threads = context->num_threads;
#pragma omp parallel for num_threads(num_threads)
#endif
- for ( int64_t t = 0; t < static_cast<int64_t>(context->numpacks); ++t )
+ for ( int64_t t = 0; t < lnumpacks; ++t )
baseSortRequests[t].dispatch();
}
};
=====================================
src/libmaus2/util/StackLineTranslator.hpp
=====================================
@@ -0,0 +1,33 @@
+/*
+ libmaus2
+ Copyright (C) 2020 German Tischler-Höhle
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>..
+*/
+#if ! defined(LIBMAUS2_UTIL_STACKLINETRANSLATOR_HPP)
+#define LIBMAUS2_UTIL_STACKLINETRANSLATOR_HPP
+
+#include <string>
+
+namespace libmaus2
+{
+ namespace util
+ {
+ struct StackLineTranslator
+ {
+ static std::string translate(char const * p, int const deep);
+ };
+ }
+}
+#endif
=====================================
src/libmaus2/util/StackTrace.cpp
=====================================
@@ -18,6 +18,7 @@
*/
#include <libmaus2/util/StackTrace.hpp>
+#include <libmaus2/util/StackLineTranslator.hpp>
#if defined(__linux__)
#include <libmaus2/util/PosixExecute.hpp>
#endif
@@ -56,7 +57,7 @@ static std::string readCommandLine()
if ( ! istr_cmdline.is_open() )
return std::string();
- std::ostringstream ocmdline;
+ std::ostringstream ocmdline;
int c;
while ( (c=istr_cmdline.get()) != std::istream::traits_type::eof() )
ocmdline.put(c);
@@ -112,6 +113,9 @@ translate
std::pair < std::string, std::string > B = components(A.first,'(',')');
#if defined(LIBMAUS2_DEBUG_COMPILED)
+ #if 1
+ ostr << libmaus2::util::StackLineTranslator::translate(trace[i].c_str(),1 /* deep */) << std::endl;
+ #else
std::string const execname = findIfSelf(B.first);
std::string const & addr = A.second;
@@ -148,6 +152,7 @@ translate
//ostr << B.first << "(" << B.second << ")" << "[" << A.second << ":" << addrout << "]\n";
ostr << execname << "(" << B.second << ")" << "[" << A.second << ":" << addrout << "]\n";
+ #endif
#else
if ( B.second.find_last_of('+') != std::string::npos )
{
=====================================
src/libmaus2/util/StackTraceBufferContainer.cpp
=====================================
@@ -0,0 +1,531 @@
+/*
+ libmaus2
+ Copyright (C) 2009-2013 German Tischler
+ Copyright (C) 2011-2013 Genome Research Limited
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>..
+*/
+#if defined(LIBMAUS2_HAVE_LIBUNWIND_H)
+#include <libunwind.h>
+#endif
+
+#if defined(LIBMAUS2_HAVE_EXECINFO_H)
+#include <execinfo.h>
+#endif
+
+#include <setjmp.h>
+
+#include <libmaus2/util/StackTraceBufferContainer.hpp>
+#include <libmaus2/util/StackLineTranslator.hpp>
+#include <libmaus2/aio/StreamLock.hpp>
+
+void libmaus2::util::StackTraceBufferContainer::reset()
+{
+ numtraces = 0;
+ signal(SIGSEGV,prevsig);
+}
+
+int libmaus2::util::StackTraceBufferContainer::setup()
+{
+ numtraces = 0;
+
+ prevsig = signal(SIGSEGV,sigseghandler);
+
+ if ( setjmp(segenv) )
+ {
+ // signal(SIGSEGV,prevsig);
+
+ {
+ std::cerr << "[E] libmaus2::util::StackTraceBufferContainer: setjmp returned non zero (segfault)" << std::endl;
+
+ std::thread::id const id = ::std::this_thread::get_id();
+
+ std::size_t const loopend = std::min(
+ static_cast<std::size_t>(StackTraceBufferContainer_MAXTRACES),
+ static_cast<std::size_t>(numtraces)
+ );
+
+ for ( ::std::size_t i = 0; i < loopend; ++i )
+ if ( traces[i].first == id )
+ {
+ StackTraceBuffer & buf = traces[i].second;
+
+ if ( buf.stacktracebufn > 0 )
+ {
+ #if defined(LIBMAUS2_HAVE_EXECINFO_H) && defined(LIBMAUS2_HAVE_BACKTRACE)
+ char ** syms = backtrace_symbols(&buf.stacktracebuf[0],buf.stacktracebufn);
+
+ for ( int i = 0; i < buf.stacktracebufn; ++i )
+ {
+ std::string const s = StackLineTranslator::translate(syms[i],itranslate);
+ std::cerr << "[" << i << "]=" << s << "\n";
+ }
+
+ free(syms);
+ #endif
+ }
+
+ }
+ }
+
+ abort();
+ }
+
+ return 0;
+}
+
+#if defined(LIBMAUS2_HAVE_UNISTD_H)
+#include <unistd.h>
+#endif
+
+#include <cstring>
+
+void libmaus2::util::StackTraceBufferContainer::sigseghandler(int)
+{
+ uint64_t const traceid = __sync_fetch_and_add(&numtraces,1);
+
+ // if ( traceid < StackTraceBufferContainer_MAXTRACES )
+ if ( !traceid )
+ {
+ std::thread::id const id = ::std::this_thread::get_id();
+ traces[traceid].first = id;
+
+ #if defined(LIBMAUS2_HAVE_EXECINFO_H) && defined(LIBMAUS2_HAVE_BACKTRACE)
+ StackTraceBuffer & lbuf = traces[traceid].second;
+ lbuf.stacktracebufn = backtrace(&(lbuf.stacktracebuf[0]),StackTraceBufferContainer_STACKTRACEBUFSIZE);
+ #endif
+
+ longjmp(segenv,1);
+ }
+ else
+ {
+ while ( true )
+ {
+ ::sleep(1);
+ }
+ }
+}
+
+template<typename type>
+struct Array
+{
+ type * p;
+
+ void allocate(::std::size_t const n)
+ {
+ try
+ {
+ p = new type[n];
+ }
+ catch(...)
+ {
+ p = nullptr;
+ }
+ }
+
+ Array()
+ : p(nullptr)
+ {
+
+ }
+
+ Array(::std::size_t const n)
+ : p(nullptr)
+ {
+ allocate(n);
+ }
+
+ ~Array()
+ {
+ if ( p )
+ delete [] p;
+ }
+};
+
+#include <sstream>
+
+#if defined(LIBMAUS2_HAVE_SYS_TYPES_H)
+#include <sys/types.h>
+#endif
+
+#if defined(LIBMAUS2_HAVE_SYS_WAIT_H)
+#include <sys/wait.h>
+#endif
+
+#if defined(LIBMAUS2_HAVE_UNISTD_H)
+#include <unistd.h>
+#endif
+
+#if defined(LIBMAUS2_HAVE_FCNTL_H)
+#include <fcntl.h>
+#endif
+
+#include <vector>
+
+#include <cstdlib>
+#include <cstring>
+#include <libmaus2/util/Demangle.hpp>
+
+static int callCommand(std::vector<std::string> const & V, std::string const & outtmp, std::string & r)
+{
+ int rmk = -1;
+ int ex = EXIT_SUCCESS;
+ char * cp = nullptr;
+ pid_t pid = -1;
+ size_t todo = 0;
+ char * pp = nullptr;
+ off_t fs = 0;
+ off_t fs0 = 0;
+ size_t s = 0;
+
+ for ( uint64_t i = 0; i < V.size(); ++i )
+ s += V[i].size()+1;
+
+ Array<char> Atemp(outtmp.size()+1);
+ Array<char> Ctemp(s);
+ Array<char *> Ptemp(V.size()+1);
+ Array<char> T;
+
+ if ( ! Atemp.p )
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+ ::std::fill(Atemp.p,Atemp.p+outtmp.size()+1,0);
+ ::std::copy(outtmp.begin(),outtmp.end(),Atemp.p);
+
+
+ if ( ! Ctemp.p )
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+ if ( ! Ptemp.p )
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+ cp = Ctemp.p;
+ for ( uint64_t i = 0; i < V.size(); ++i )
+ {
+ Ptemp.p[i] = cp;
+ std::size_t const l = V[i].size();
+ std::copy(V[i].begin(),V[i].end(),cp);
+ cp += l;
+ *(cp++) = 0;
+ }
+ Ptemp.p[V.size()] = nullptr;
+
+ rmk = mkstemp(Atemp.p);
+
+ if ( rmk < 0 )
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+
+ pid = fork();
+
+ if ( pid == static_cast<pid_t>(-1) )
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+ else if ( pid == 0 )
+ {
+ int const nullfd = ::open("/dev/null",O_WRONLY);
+
+ if ( nullfd < 0 )
+ _exit(EXIT_FAILURE);
+
+ ::close(STDOUT_FILENO);
+ ::close(STDERR_FILENO);
+
+ int const rdup = ::dup2(rmk,STDOUT_FILENO);
+
+ if ( rdup < 0 )
+ _exit(EXIT_FAILURE);
+
+ int const rdup2 = ::dup2(nullfd,STDERR_FILENO);
+ if ( rdup2 < 0 )
+ _exit(EXIT_FAILURE);
+
+ execv(Ptemp.p[0],Ptemp.p);
+
+ _exit(EXIT_FAILURE);
+ }
+
+ int status;
+ while ( true )
+ {
+ pid_t const rpid = waitpid(pid,&status,0);
+
+ if ( rpid == pid )
+ break;
+ else if ( rpid == static_cast<pid_t>(-1) )
+ {
+ int const error = errno;
+
+ switch ( error )
+ {
+ case EINTR:
+ case EAGAIN:
+ break;
+ default:
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+ }
+ }
+ }
+
+ if ( status != 0 )
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+
+ fs = lseek(rmk,0,SEEK_END);
+
+ if ( fs == static_cast<off_t>(-1) )
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+
+ fs0 = lseek(rmk,0,SEEK_SET);
+
+ if ( fs0 == static_cast<off_t>(-1) )
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+
+ T.allocate(fs);
+ if ( ! T.p )
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+ pp = T.p;
+ todo = fs;
+
+ while ( todo )
+ {
+ ::ssize_t const r = ::read(rmk,pp,todo);
+
+ if ( r < 0 )
+ {
+ int const error = errno;
+ switch ( error )
+ {
+ case EINTR:
+ case EAGAIN:
+ break;
+ default:
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+ }
+ }
+ else if ( r == 0 )
+ {
+ ex = EXIT_FAILURE;
+ goto cleanup;
+ }
+ else
+ {
+ pp += r;
+ todo -= r;
+ }
+ }
+
+ r = std::string(T.p,T.p+fs);
+
+ cleanup:
+ if ( rmk >= 0 )
+ {
+ ::close(rmk);
+ ::remove(Atemp.p);
+ rmk = -1;
+ }
+
+ return ex;
+}
+
+std::string libmaus2::util::StackLineTranslator::translate(char const * ip, int const deep)
+{
+ // /home/baer/src/git/libmaus2/src/.libs/libmaus2.so.2(_ZN8libmaus24util25StackTraceBufferContainer13sigseghandlerEi+0x70) [0x7f328cc1e980]
+ if ( ! ip )
+ return std::string();
+
+ char const * path_a = ip;
+ char const * path_e = path_a;
+
+ while ( *path_e && *path_e != '(' )
+ ++path_e;
+
+ if ( !*path_e )
+ return std::string(ip);
+
+ char const * symoffstart = path_e+1;
+ char const * symoffend = symoffstart;
+
+ while ( *symoffend && *symoffend != ')' )
+ ++symoffend;
+
+ if ( !*symoffend )
+ return std::string(ip);
+
+ char const * symstart = symoffstart;
+ char const * symend = symstart;
+
+ while ( symend != symoffend && *symend != '+' )
+ ++symend;
+
+ if ( symend == symoffend )
+ return std::string(ip);
+
+ char const * offstart = symend+1;
+ char const * offend = symoffend;
+
+ std::string const path(path_a,path_e);
+ std::string const symoff(symoffstart,symoffend);
+ std::string const sym(symstart,symend);
+ std::string const off(offstart,offend);
+
+ std::string p = path + "(" + libmaus2::util::Demangle::demangleName(sym) + "+" + off + ")";
+
+ if ( ! deep )
+ return p;
+
+ std::string const tmpprefix = "/tmp/libmaus2_";
+ std::ostringstream nmtmpostr;
+ #if defined(LIBMAUS2_HAVE_GETPID)
+ nmtmpostr << tmpprefix << getpid() << "_XXXXXX";
+ #else
+ nmtmpostr << tmpprefix << "_XXXXXX";
+ #endif
+ std::string const nmtmp = nmtmpostr.str();
+
+ std::vector<std::string> Vcom;
+ Vcom.push_back("/usr/bin/nm");
+ Vcom.push_back(path);
+
+ std::string rnm;
+ int const r_nm = callCommand(Vcom,nmtmp,rnm);
+
+ if ( r_nm != EXIT_SUCCESS )
+ return p;
+
+ // std::cerr << "path=" << path << " symoff=" << symoff << " sym=" << sym << " off=" << off << " nmtmp=" << nmtmp << std::endl;
+
+ uint64_t uaddr = 0;
+ bool haveaddr = false;
+
+ std::istringstream nm_istr(rnm);
+ std::string line;
+ while ( std::getline(nm_istr,line) )
+ {
+ uint64_t low = 0;
+ std::vector<std::string> V;
+ while ( low < line.size() )
+ {
+ while ( low < line.size() && isspace(line[low]) )
+ ++low;
+
+ if ( low < line.size() )
+ {
+ uint64_t high = low+1;
+ while ( high < line.size() && !isspace(line[high]) )
+ ++high;
+
+ V.push_back(line.substr(low,high-low));
+
+ low = high;
+ }
+ }
+ if ( 2 < V.size() && V[2] == sym )
+ {
+ std::string const saddr = V[0];
+
+ char const * pa = saddr.c_str();
+ char const * pe = pa + saddr.size();
+
+ while ( pa != pe && *pa == '0' )
+ ++pa;
+
+ std::string const laddr(pa,pe);
+
+ if ( laddr.size() )
+ {
+ // std::string const paddr = std::string("0x")+laddr;
+ std::istringstream istr(laddr);
+ uint64_t luaddr;
+ istr >> std::hex >> luaddr;
+
+ if ( istr && istr.peek() == std::istream::traits_type::eof() )
+ {
+ uaddr = luaddr;
+ haveaddr = true;
+ }
+ }
+ }
+ }
+
+ if ( sym.size() && ! haveaddr )
+ return p;
+
+
+ if ( off.size() < 2 || off.substr(0,2) != "0x" )
+ return p;
+
+ std::istringstream offistr(off.substr(2));
+ uint64_t uoff;
+ offistr >> std::hex >> uoff;
+ if ( !offistr && offistr.peek() != std::istream::traits_type::eof() )
+ return p;
+
+ std::ostringstream addrostr;
+ addrostr << "0x" << std::hex << (uaddr+uoff);
+ std::string const addr = addrostr.str();
+
+ std::vector<std::string> Vaddr;
+ Vaddr.push_back("/usr/bin/addr2line");
+ Vaddr.push_back("-f");
+ Vaddr.push_back("-e");
+ Vaddr.push_back(path);
+ Vaddr.push_back(addr);
+
+ std::string raddrline;
+ int const r_addrline = callCommand(Vaddr,nmtmp,raddrline);
+
+ if ( r_addrline != EXIT_SUCCESS )
+ return p;
+
+ std::vector<std::string> Vad;
+ std::istringstream adistr(raddrline);
+ while ( std::getline(adistr,line) )
+ Vad.push_back(line);
+
+ if ( Vad.size() < 2 )
+ return p;
+
+ std::ostringstream outostr;
+ outostr << path << "(" << libmaus2::util::Demangle::demangleName(Vad[0]) << "+" << off << ")" << "[" << Vad[1] << "]";
+
+ return outostr.str();
+}
=====================================
src/libmaus2/util/StackTraceBufferContainer.hpp
=====================================
@@ -0,0 +1,65 @@
+/*
+ libmaus2
+ Copyright (C) 2020 German Tischler-Höhle
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>..
+*/
+#if ! defined(LIBMAUS2_UTIL_STACKTRACEBUFFERCONTAINER_HPP)
+#define LIBMAUS2_UTIL_STACKTRACEBUFFERCONTAINER_HPP
+
+#include <libmaus2/LibMausConfig.hpp>
+
+#include <csignal>
+#include <iostream>
+#include <thread>
+#include <utility>
+#include <atomic>
+#include <setjmp.h>
+
+namespace libmaus2
+{
+ namespace util
+ {
+ struct StackTraceBufferContainer
+ {
+ #define StackTraceBufferContainer_STACKTRACEBUFSIZE 30
+ #define StackTraceBufferContainer_MAXTRACES 32
+
+ typedef void * stacktracebuf_t[StackTraceBufferContainer_STACKTRACEBUFSIZE];
+
+ struct StackTraceBuffer
+ {
+ stacktracebuf_t stacktracebuf;
+ int stacktracebufn;
+
+ StackTraceBuffer() : stacktracebufn(0) {}
+ };
+
+ typedef std::pair<std::thread::id,StackTraceBuffer> id_trace_type;
+
+ static id_trace_type traces[StackTraceBufferContainer_MAXTRACES];
+ static std::size_t volatile numtraces;
+
+ static jmp_buf segenv;
+ static sighandler_t prevsig;
+ static int init;
+ static int itranslate;
+
+ static int setup();
+ static void reset();
+ static void sigseghandler(int);
+ };
+ }
+}
+#endif
=====================================
src/libmaus2/util/TabEntry.hpp
=====================================
@@ -124,12 +124,37 @@ namespace libmaus2
return std::pair<char const *,char const *>(a+LP.first,a+LP.second);
}
+ std::pair<char const *,char const *> getUnquoted(uint64_t const i, char const * a) const
+ {
+ P LP = (*this)[i];
+
+ if (
+ (LP.second - LP.first >= 2)
+ &&
+ a[LP.first] == quote_sym
+ &&
+ a[LP.second-1] == quote_sym
+ )
+ {
+ LP.first += 1;
+ LP.second -= 1;
+ }
+
+ return std::pair<char const *,char const *>(a+LP.first,a+LP.second);
+ }
+
std::string getString(uint64_t const i, char const * a) const
{
std::pair<char const *,char const *> const P = get(i,a);
return std::string(P.first,P.second);
}
+ std::string getUnquotedString(uint64_t const i, char const * a) const
+ {
+ std::pair<char const *,char const *> const P = getUnquoted(i,a);
+ return std::string(P.first,P.second);
+ }
+
std::vector<std::string> getStrings(char const * a) const
{
std::vector<std::string> V(size());
@@ -138,6 +163,14 @@ namespace libmaus2
return V;
}
+ std::vector<std::string> getUnquotedStrings(char const * a) const
+ {
+ std::vector<std::string> V(size());
+ for ( uint64_t i = 0; i < size(); ++i )
+ V[i] = getUnquotedString(i,a);
+ return V;
+ }
+
template<typename value_type>
value_type getParsed(uint64_t const i, char const * a) const
{
=====================================
src/libmaus2/vcf/VCFParser.hpp
=====================================
@@ -1009,6 +1009,49 @@ namespace libmaus2
return out;
}
+ static std::ostream & runFilterFilterFlags(std::istream & in, std::ostream & out, std::vector<std::string> const & Vfilter)
+ {
+ libmaus2::trie::Trie<char> TR;
+ TR.insertContainer(Vfilter);
+ ::libmaus2::trie::LinearHashTrie<char,uint32_t>::unique_ptr_type LHT(TR.toLinearHashTrie<uint32_t>());
+
+ VCFParser VCF(in);
+ VCF.printText(out);
+
+ std::pair<bool, char const *> E;
+ libmaus2::util::TabEntry<> T;
+ libmaus2::util::TabEntry<';'> TI;
+
+ while ( (E=VCF.readEntry(T)).first )
+ {
+ if ( 6 < T.size() )
+ {
+ std::pair<char const *,char const *> IP = T.get(6,E.second);
+ TI.parse(IP.first,IP.first,IP.second);
+
+ bool ok = false;
+ for ( uint64_t i = 0; i < TI.size(); ++i )
+ {
+ std::pair<char const *,char const *> P = TI.get(i,IP.first);
+
+ int64_t const id = LHT->searchCompleteNoFailure(P.first,P.second);
+ if ( id >= 0 )
+ ok = true;
+ }
+
+ if ( ok )
+ {
+ char const * a = E.second;
+ char const * e = T.get(T.size()-1,a).second;
+ out.write(a,e-a);
+ out.put('\n');
+ }
+ }
+ }
+
+ return out;
+ }
+
static std::ostream & runFilterInfo(std::istream & in, std::ostream & out, std::string const & filter)
{
@@ -1022,6 +1065,18 @@ namespace libmaus2
return runFilterInfo(in,out,Vfilter);
}
+ static std::ostream & runFilterFilterFlags(std::istream & in, std::ostream & out, std::string const & filter)
+ {
+ libmaus2::util::TabEntry<';'> TE;
+ TE.parse(filter.c_str(),filter.c_str(),filter.c_str()+filter.size());
+
+ std::vector<std::string> Vfilter;
+ for ( uint64_t i = 0; i < TE.size(); ++i )
+ Vfilter.push_back(TE.getString(i,filter.c_str()));
+
+ return runFilterFilterFlags(in,out,Vfilter);
+ }
+
static std::ostream & runFilterSamples(std::istream & in, std::ostream & out, std::vector<std::string> const & Vfilter)
{
libmaus2::trie::Trie<char> TR;
@@ -1199,7 +1254,9 @@ namespace libmaus2
uint64_t const samplenum,
libmaus2::autoarray::AutoArray<
std::pair<
+ // key
std::pair<char const *,char const *>,
+ // value
std::pair<char const *,char const *>
> > & A
)
@@ -1287,6 +1344,7 @@ namespace libmaus2
return std::string(P.first,P.second);
}
+ template<char separator>
static uint64_t getSampleValueVectorForKey(
std::string const & key,
libmaus2::util::TabEntry<> const & T,
@@ -1299,7 +1357,7 @@ namespace libmaus2
std::pair<char const *,char const *>,
std::pair<char const *,char const *>
> > & A,
- libmaus2::util::TabEntry<','> & TC,
+ libmaus2::util::TabEntry<separator> & TC,
libmaus2::autoarray::AutoArray< std::pair<char const *,char const *> > & O
)
{
@@ -1318,7 +1376,7 @@ namespace libmaus2
return TC.size();
}
- template<typename type>
+ template<typename type, char separator = ','>
static uint64_t getSampleValueVectorForKeyParsed(
std::string const & key,
libmaus2::util::TabEntry<> const & T,
@@ -1331,7 +1389,7 @@ namespace libmaus2
std::pair<char const *,char const *>,
std::pair<char const *,char const *>
> > & A,
- libmaus2::util::TabEntry<','> & TC,
+ libmaus2::util::TabEntry<separator> & TC,
libmaus2::autoarray::AutoArray< type > & O
)
{
@@ -1364,7 +1422,7 @@ namespace libmaus2
return TC.size();
}
- template<typename type>
+ template<typename type, char separator = ','>
static std::vector<type> getSampleValueVectorForKeyParsed(
std::string const & key,
libmaus2::util::TabEntry<> const & T,
@@ -1379,7 +1437,7 @@ namespace libmaus2
std::pair<char const *,char const *>,
std::pair<char const *,char const *>
> > A;
- libmaus2::util::TabEntry<','> TC;
+ libmaus2::util::TabEntry<separator> TC;
libmaus2::autoarray::AutoArray< type > O;
uint64_t const o = getSampleValueVectorForKeyParsed(key,T,a,TSC0,TSC1,samplenum,A,TC,O);
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/compare/56cf1bc6ab6461d9daf582a07427ed25132881a0...a7bebcba662860f622a4c62cdf88e4be6db7ab38
--
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/compare/56cf1bc6ab6461d9daf582a07427ed25132881a0...a7bebcba662860f622a4c62cdf88e4be6db7ab38
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200528/1d6cf068/attachment-0001.html>
More information about the debian-med-commit
mailing list