ChangeLog

+libmaus2 (2.0.657-1) unstable; urgency=medium
+
+  * allow limiting parallelism in fragment merging of BlockSortControl (implicitely reduces number of open files)
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Mon, 19 Aug 2019 14:29:09 +0200
+
+libmaus2 (2.0.656-1) unstable; urgency=medium
+
+  * refactoring socket classes
+  * refactor and guard against interupted system calls in Socket.hpp
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 16 Aug 2019 10:54:29 +0200
+
+libmaus2 (2.0.655-1) unstable; urgency=medium
+
+  * refactor AutoArray and avoid mismatching alloc/dealloc pairs (do not deallocate memory allocated through new [] using free)
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 15 Aug 2019 21:20:31 +0200
+
+libmaus2 (2.0.654-1) unstable; urgency=medium
+
+  * remove extraneous include directive in SkewSuffixSort
+  * add missing include directive in TempFileArray
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 13 Aug 2019 15:58:13 +0200
+
 libmaus2 (2.0.653-1) unstable; urgency=medium
 
   * add getNextReferenceLength/getNextFrontDel/getNextReferenceInterval in BamAlignmentDecoderBase/BamAlignment

autom4te.cache/output.0

 @%:@! /bin/sh
 @%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.652.
+@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.656.
 @%:@
 @%:@ Report bugs to <tischler@mpi-cbg.de>.
 @%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libmaus2'
 PACKAGE_TARNAME='libmaus2'
-PACKAGE_VERSION='2.0.652'
-PACKAGE_STRING='libmaus2 2.0.652'
+PACKAGE_VERSION='2.0.656'
+PACKAGE_STRING='libmaus2 2.0.656'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1609,7 +1609,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures libmaus2 2.0.652 to adapt to many kinds of systems.
+\`configure' configures libmaus2 2.0.656 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1681,7 +1681,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libmaus2 2.0.652:";;
+     short | recursive ) echo "Configuration of libmaus2 2.0.656:";;
    esac
   cat <<\_ACEOF
@@ -1851,7 +1851,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libmaus2 configure 2.0.652
+libmaus2 configure 2.0.656
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2724,7 +2724,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
-It was created by libmaus2 $as_me 2.0.652, which was
+It was created by libmaus2 $as_me 2.0.656, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -3072,7 +3072,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
-LIBRARY_VERSION=2:652:0
+LIBRARY_VERSION=2:656:0
 { $as_echo "$as_me:${as_lineno-$LINENO}: Configuring for source in directory ${srcdir}" >&5
 $as_echo "$as_me: Configuring for source in directory ${srcdir}" >&6;}
 ac_aux_dir=
@@ -12628,7 +12628,7 @@ fi
 # Define the identity of the package.
  PACKAGE='libmaus2'
- VERSION='2.0.652'
+ VERSION='2.0.656'
 cat >>confdefs.h <<_ACEOF
@@ -28157,7 +28157,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by libmaus2 $as_me 2.0.652, which was
+This file was extended by libmaus2 $as_me 2.0.656, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -28224,7 +28224,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-libmaus2 config.status 2.0.652
+libmaus2 config.status 2.0.656
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

autom4te.cache/output.1

 @%:@! /bin/sh
 @%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.653.
+@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.657.
 @%:@
 @%:@ Report bugs to <tischler@mpi-cbg.de>.
 @%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libmaus2'
 PACKAGE_TARNAME='libmaus2'
-PACKAGE_VERSION='2.0.653'
-PACKAGE_STRING='libmaus2 2.0.653'
+PACKAGE_VERSION='2.0.657'
+PACKAGE_STRING='libmaus2 2.0.657'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1609,7 +1609,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures libmaus2 2.0.653 to adapt to many kinds of systems.
+\`configure' configures libmaus2 2.0.657 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1681,7 +1681,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libmaus2 2.0.653:";;
+     short | recursive ) echo "Configuration of libmaus2 2.0.657:";;
    esac
   cat <<\_ACEOF
@@ -1851,7 +1851,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libmaus2 configure 2.0.653
+libmaus2 configure 2.0.657
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2724,7 +2724,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
-It was created by libmaus2 $as_me 2.0.653, which was
+It was created by libmaus2 $as_me 2.0.657, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -3072,7 +3072,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
-LIBRARY_VERSION=2:653:0
+LIBRARY_VERSION=2:657:0
 { $as_echo "$as_me:${as_lineno-$LINENO}: Configuring for source in directory ${srcdir}" >&5
 $as_echo "$as_me: Configuring for source in directory ${srcdir}" >&6;}
 ac_aux_dir=
@@ -12628,7 +12628,7 @@ fi
 # Define the identity of the package.
  PACKAGE='libmaus2'
- VERSION='2.0.653'
+ VERSION='2.0.657'
 cat >>confdefs.h <<_ACEOF
@@ -28157,7 +28157,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by libmaus2 $as_me 2.0.653, which was
+This file was extended by libmaus2 $as_me 2.0.657, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -28224,7 +28224,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-libmaus2 config.status 2.0.653
+libmaus2 config.status 2.0.657
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

autom4te.cache/output.2

 @%:@! /bin/sh
 @%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.653.
+@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.657.
 @%:@
 @%:@ Report bugs to <tischler@mpi-cbg.de>.
 @%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libmaus2'
 PACKAGE_TARNAME='libmaus2'
-PACKAGE_VERSION='2.0.653'
-PACKAGE_STRING='libmaus2 2.0.653'
+PACKAGE_VERSION='2.0.657'
+PACKAGE_STRING='libmaus2 2.0.657'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1609,7 +1609,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures libmaus2 2.0.653 to adapt to many kinds of systems.
+\`configure' configures libmaus2 2.0.657 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1681,7 +1681,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libmaus2 2.0.653:";;
+     short | recursive ) echo "Configuration of libmaus2 2.0.657:";;
    esac
   cat <<\_ACEOF
@@ -1851,7 +1851,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libmaus2 configure 2.0.653
+libmaus2 configure 2.0.657
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2724,7 +2724,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
-It was created by libmaus2 $as_me 2.0.653, which was
+It was created by libmaus2 $as_me 2.0.657, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -3072,7 +3072,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
-LIBRARY_VERSION=2:653:0
+LIBRARY_VERSION=2:657:0
 { $as_echo "$as_me:${as_lineno-$LINENO}: Configuring for source in directory ${srcdir}" >&5
 $as_echo "$as_me: Configuring for source in directory ${srcdir}" >&6;}
 ac_aux_dir=
@@ -12628,7 +12628,7 @@ fi
 # Define the identity of the package.
  PACKAGE='libmaus2'
- VERSION='2.0.653'
+ VERSION='2.0.657'
 cat >>confdefs.h <<_ACEOF
@@ -28157,7 +28157,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by libmaus2 $as_me 2.0.653, which was
+This file was extended by libmaus2 $as_me 2.0.657, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -28224,7 +28224,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-libmaus2 config.status 2.0.653
+libmaus2 config.status 2.0.657
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

autom4te.cache/traces.1

@@ -4,7 +4,7 @@ m4trace:aclocal.m4:1460: -1- m4_include([m4/ltoptions.m4])
 m4trace:aclocal.m4:1461: -1- m4_include([m4/ltsugar.m4])
 m4trace:aclocal.m4:1462: -1- m4_include([m4/ltversion.m4])
 m4trace:aclocal.m4:1463: -1- m4_include([m4/lt~obsolete.m4])
-m4trace:configure.ac:1: -1- AC_INIT([libmaus2], [2.0.653], [tischler@mpi-cbg.de], [libmaus2], [https://github.com/gt1/libmaus2])
+m4trace:configure.ac:1: -1- AC_INIT([libmaus2], [2.0.657], [tischler@mpi-cbg.de], [libmaus2], [https://github.com/gt1/libmaus2])
 m4trace:configure.ac:1: -1- m4_pattern_forbid([^_?A[CHUM]_])
 m4trace:configure.ac:1: -1- m4_pattern_forbid([_AC_])
 m4trace:configure.ac:1: -1- m4_pattern_forbid([^LIBOBJS$], [do not use LIBOBJS directly, use AC_LIBOBJ (see section `AC_LIBOBJ vs LIBOBJS'])

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for libmaus2 2.0.653.
+# Generated by GNU Autoconf 2.69 for libmaus2 2.0.657.
 #
 # Report bugs to <tischler@mpi-cbg.de>.
 #
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libmaus2'
 PACKAGE_TARNAME='libmaus2'
-PACKAGE_VERSION='2.0.653'
-PACKAGE_STRING='libmaus2 2.0.653'
+PACKAGE_VERSION='2.0.657'
+PACKAGE_STRING='libmaus2 2.0.657'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1609,7 +1609,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures libmaus2 2.0.653 to adapt to many kinds of systems.
+\`configure' configures libmaus2 2.0.657 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1681,7 +1681,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libmaus2 2.0.653:";;
+     short | recursive ) echo "Configuration of libmaus2 2.0.657:";;
    esac
   cat <<\_ACEOF
@@ -1851,7 +1851,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libmaus2 configure 2.0.653
+libmaus2 configure 2.0.657
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2724,7 +2724,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
-It was created by libmaus2 $as_me 2.0.653, which was
+It was created by libmaus2 $as_me 2.0.657, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -3072,7 +3072,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
-LIBRARY_VERSION=2:653:0
+LIBRARY_VERSION=2:657:0
 { $as_echo "$as_me:${as_lineno-$LINENO}: Configuring for source in directory ${srcdir}" >&5
 $as_echo "$as_me: Configuring for source in directory ${srcdir}" >&6;}
 ac_aux_dir=
@@ -12628,7 +12628,7 @@ fi
 # Define the identity of the package.
  PACKAGE='libmaus2'
- VERSION='2.0.653'
+ VERSION='2.0.657'
 cat >>confdefs.h <<_ACEOF
@@ -28157,7 +28157,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by libmaus2 $as_me 2.0.653, which was
+This file was extended by libmaus2 $as_me 2.0.657, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -28224,7 +28224,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-libmaus2 config.status 2.0.653
+libmaus2 config.status 2.0.657
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

configure.ac

-AC_INIT(libmaus2,2.0.653,[tischler@mpi-cbg.de],[libmaus2],[https://github.com/gt1/libmaus2])
-LIBRARY_VERSION=2:653:0
+AC_INIT(libmaus2,2.0.657,[tischler@mpi-cbg.de],[libmaus2],[https://github.com/gt1/libmaus2])
+LIBRARY_VERSION=2:657:0
 AC_MSG_NOTICE([Configuring for source in directory ${srcdir}])
 AC_CANONICAL_SYSTEM
 AC_CANONICAL_HOST

debian/changelog

+libmaus2 (2.0.657-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Andreas Tille <tille@debian.org>  Mon, 19 Aug 2019 18:18:32 +0200
+
 libmaus2 (2.0.653-1) unstable; urgency=medium
 
   * New upstream version

src/Makefile.am

@@ -1773,7 +1773,9 @@ libmaus2rmq_include_HEADERS=\
 
 libmaus2network_includedir=$(includedir)/libmaus2/network
 libmaus2network_include_HEADERS=\
-	libmaus2/network/Socket.hpp \
+	libmaus2/network/SocketBase.hpp \
+	libmaus2/network/ClientSocket.hpp \
+	libmaus2/network/ServerSocket.hpp \
 	libmaus2/network/GetHostName.hpp \
 	libmaus2/network/SocketInputStreamBuffer.hpp \
 	libmaus2/network/SocketInputStream.hpp \

src/Makefile.in

@@ -4173,7 +4173,9 @@ libmaus2rmq_include_HEADERS = \
 libmaus2network_includedir = $(includedir)/libmaus2/network
 libmaus2network_include_HEADERS = \
-	libmaus2/network/Socket.hpp \
+	libmaus2/network/SocketBase.hpp \
+	libmaus2/network/ClientSocket.hpp \
+	libmaus2/network/ServerSocket.hpp \
 	libmaus2/network/GetHostName.hpp \
 	libmaus2/network/SocketInputStreamBuffer.hpp \
 	libmaus2/network/SocketInputStream.hpp \

src/libmaus2/aio/TempFileArray.hpp

@@ -22,6 +22,7 @@
 #include <libmaus2/autoarray/AutoArray.hpp>
 #include <libmaus2/util/TempFileRemovalContainer.hpp>
 #include <libmaus2/sorting/SortingBufferedOutputFile.hpp>
+#include <libmaus2/util/Concat.hpp>
 
 namespace libmaus2
 {

src/libmaus2/bambam/ReadEndsBlockIndexSet.hpp

@@ -33,12 +33,8 @@ namespace libmaus2
 {
 	namespace bambam
 	{
-		struct ReadEndsBlockIndexSet
+		struct ReadEndsBlockIndexSetBase
 		{
-			typedef ReadEndsBlockIndexSet this_type;
-			typedef libmaus2::util::unique_ptr<this_type>::type unique_ptr_type;
-			typedef libmaus2::util::shared_ptr<this_type>::type shared_ptr_type;
-
 			typedef libmaus2::index::ExternalMemoryIndexDecoder<
 				libmaus2::bambam::ReadEndsBase,
 				libmaus2::bambam::ReadEndsContainerBase::baseIndexShift,
@@ -54,55 +50,124 @@ namespace libmaus2
 				return numblocks;
 			}
 
-			std::vector<ReadEndsBlockDecoderBaseCollectionInfoBase> const info;
-			uint64_t const numblocks;
-			std::vector<uint64_t> O;
-			libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type> indexstreams;
-			libmaus2::autoarray::AutoArray<index_decoder_pointer_type> indexes;
-
-			ReadEndsBlockIndexSet(std::vector<ReadEndsBlockDecoderBaseCollectionInfoBase> const & rinfo)
-			: info(rinfo), numblocks(computeNumBlocks(rinfo)), O(rinfo.size()), indexstreams(rinfo.size()), indexes(numblocks)
+			static std::vector<uint64_t> computeO(std::vector<ReadEndsBlockDecoderBaseCollectionInfoBase> const & info)
 			{
+				std::vector<uint64_t> O(info.size());
+
 				for ( uint64_t i = 1; i < O.size(); ++i )
-					O[i] = O[i-1] + rinfo[i-1].indexoffset.size();
+					O[i] = O[i-1] + info[i-1].indexoffset.size();
 
-				for ( uint64_t i = 0; i < rinfo.size(); ++i )
+				return O;
+			}
+
+			static libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type>::unique_ptr_type openIndexStreams(
+				std::vector<ReadEndsBlockDecoderBaseCollectionInfoBase> const & info
+			)
+			{
+				libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type>::unique_ptr_type indexstreams(
+					new libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type>(info.size())
+				);
+
+				for ( uint64_t i = 0; i < info.size(); ++i )
 				{
 					libmaus2::aio::InputStreamInstance::unique_ptr_type tptr(
-						new libmaus2::aio::InputStreamInstance(rinfo[i].indexfilename)
+						new libmaus2::aio::InputStreamInstance(info[i].indexfilename)
+					);
+					(*indexstreams)[i] = UNIQUE_PTR_MOVE(tptr);
+				}
+
+				return indexstreams;
+			}
+
+			static uint64_t getBaseBlockSize()
+			{
+				return libmaus2::bambam::ReadEndsContainerBase::baseIndexStep;
+			}
+
+			static libmaus2::autoarray::AutoArray<index_decoder_pointer_type>::unique_ptr_type openIndexes(
+				std::vector<ReadEndsBlockDecoderBaseCollectionInfoBase> const & info,
+				libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type>::unique_ptr_type & indexstreams,
+				uint64_t const numblocks,
+				std::vector<uint64_t> const & O
+			)
+			{
+				libmaus2::autoarray::AutoArray<index_decoder_pointer_type>::unique_ptr_type indexes(
+					new libmaus2::autoarray::AutoArray<index_decoder_pointer_type>(numblocks)
 				);
-					indexstreams[i] = UNIQUE_PTR_MOVE(tptr);
 
-					for ( uint64_t j = 0; j < rinfo[i].indexoffset.size(); ++j )
+				for ( uint64_t i = 0; i < indexstreams->size(); ++i )
+				{
+					std::istream & str = *((*indexstreams)[i]);
+
+					for ( uint64_t j = 0; j < info[i].indexoffset.size(); ++j )
 					{
-						indexstreams[i]->clear();
-						indexstreams[i]->seekg(rinfo[i].indexoffset[j]);
+						str.clear();
+						str.seekg(info[i].indexoffset[j]);
 						index_decoder_pointer_type iptr(
-							new index_decoder_type(*(indexstreams[i]))
+							new index_decoder_type(str)
 						);
-						indexes[O[i] + j] = UNIQUE_PTR_MOVE(iptr);
+						(*indexes)[O[i] + j] = UNIQUE_PTR_MOVE(iptr);
 					}
 				}
+
+				return indexes;
 			}
+		};
 
-			uint64_t size() const
+		struct ReadEndsBlockIndexSetData : public ReadEndsBlockIndexSetBase
 		{
-				return numblocks;
-			}
+			typedef ReadEndsBlockIndexSetData this_type;
+			typedef libmaus2::util::unique_ptr<this_type>::type unique_ptr_type;
+			typedef libmaus2::util::shared_ptr<this_type>::type shared_ptr_type;
 
+			private:
 			index_decoder_type & operator[](uint64_t i)
 			{
-				return *(indexes[i]);
+				return *((*indexes)[i]);
+			}
+
+			public:
+			std::vector<ReadEndsBlockDecoderBaseCollectionInfoBase> const info;
+			uint64_t const numblocks;
+			std::vector<uint64_t> const O;
+
+			private:
+			libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type>::unique_ptr_type indexstreams;
+			libmaus2::autoarray::AutoArray<index_decoder_pointer_type>::unique_ptr_type indexes;
+			libmaus2::parallel::StdMutex mutex;
+
+			public:
+			ReadEndsBlockIndexSetData(std::vector<ReadEndsBlockDecoderBaseCollectionInfoBase> const & rinfo)
+			: info(rinfo), numblocks(computeNumBlocks(rinfo)), O(computeO(rinfo)), indexstreams(openIndexStreams(rinfo)), indexes(openIndexes(rinfo,indexstreams,numblocks,O)), mutex()
+			{
+			}
+
+			uint64_t size() const
+			{
+				return numblocks;
 			}
 
 			std::pair<uint64_t,uint64_t> getOffset(uint64_t const block, uint64_t const subblock)
 			{
-				return (*this)[block][subblock];
+				std::pair<uint64_t,uint64_t> P;
+				{
+					libmaus2::parallel::ScopeStdMutex smutex(mutex);
+					P = (*this)[block][subblock];
 				}
+				return P;
+			}
+		};
 
-			static uint64_t getBaseBlockSize()
+		struct ReadEndsBlockIndexSet : public ReadEndsBlockIndexSetBase
+		{
+			typedef ReadEndsBlockIndexSet this_type;
+			typedef libmaus2::util::unique_ptr<this_type>::type unique_ptr_type;
+			typedef libmaus2::util::shared_ptr<this_type>::type shared_ptr_type;
+
+			ReadEndsBlockIndexSetData & data;
+
+			ReadEndsBlockIndexSet(ReadEndsBlockIndexSetData & rdata) : data(rdata)
 			{
-				return libmaus2::bambam::ReadEndsContainerBase::baseIndexStep;
 			}
 
 			std::pair<uint64_t,uint64_t> merge(
@@ -119,29 +184,29 @@ namespace libmaus2
 					exp += V[i].second-V[i].first;
 				}
 
-				libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type> datastreams(info.size());
-				libmaus2::autoarray::AutoArray<libmaus2::lz::SnappyInputStream::unique_ptr_type> zdatastreams(size());
+				libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type> datastreams(data.info.size());
+				libmaus2::autoarray::AutoArray<libmaus2::lz::SnappyInputStream::unique_ptr_type> zdatastreams(data.size());
 				libmaus2::bambam::ReadEnds R;
 
-				for ( uint64_t i = 0; i < info.size(); ++i )
+				for ( uint64_t i = 0; i < data.info.size(); ++i )
 				{
 					// open data stream
 					libmaus2::aio::InputStreamInstance::unique_ptr_type tptr(
-						new libmaus2::aio::InputStreamInstance(info[i].datafilename)
+						new libmaus2::aio::InputStreamInstance(data.info[i].datafilename)
 					);
 					datastreams[i] = UNIQUE_PTR_MOVE(tptr);
 
 					// set up uncompressors
-					for ( uint64_t j = 0; j < info[i].indexoffset.size(); ++j )
+					for ( uint64_t j = 0; j < data.info[i].indexoffset.size(); ++j )
 					{
-						uint64_t const blockid    = O[i] + j;
+						uint64_t const blockid    = data.O[i] + j;
 						uint64_t const vlow  = V[blockid].first;
 						uint64_t const vhigh = V[blockid].second;
 						uint64_t const subblockid = vlow / getBaseBlockSize();
 
 						if ( vlow < vhigh )
 						{
-							std::pair<uint64_t,uint64_t> const zoffset = getOffset(blockid,subblockid);
+							std::pair<uint64_t,uint64_t> const zoffset = data.getOffset(blockid,subblockid);
 
 							libmaus2::lz::SnappyInputStream::unique_ptr_type zptr(
 								new libmaus2::lz::SnappyInputStream(
@@ -234,29 +299,29 @@ namespace libmaus2
 					exp += V[i].second-V[i].first;
 				}
 
-				libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type> datastreams(info.size());
-				libmaus2::autoarray::AutoArray<libmaus2::lz::SnappyInputStream::unique_ptr_type> zdatastreams(size());
+				libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type> datastreams(data.info.size());
+				libmaus2::autoarray::AutoArray<libmaus2::lz::SnappyInputStream::unique_ptr_type> zdatastreams(data.size());
 				libmaus2::bambam::ReadEnds R;
 
-				for ( uint64_t i = 0; i < info.size(); ++i )
+				for ( uint64_t i = 0; i < data.info.size(); ++i )
 				{
 					// open data stream
 					libmaus2::aio::InputStreamInstance::unique_ptr_type tptr(
-						new libmaus2::aio::InputStreamInstance(info[i].datafilename)
+						new libmaus2::aio::InputStreamInstance(data.info[i].datafilename)
 					);
 					datastreams[i] = UNIQUE_PTR_MOVE(tptr);
 
 					// set up uncompressors
-					for ( uint64_t j = 0; j < info[i].indexoffset.size(); ++j )
+					for ( uint64_t j = 0; j < data.info[i].indexoffset.size(); ++j )
 					{
-						uint64_t const blockid    = O[i] + j;
+						uint64_t const blockid    = data.O[i] + j;
 						uint64_t const vlow = V[blockid].first;
 						uint64_t const vhigh = V[blockid].second;
 
 						if ( vlow < vhigh )
 						{
 							uint64_t const subblockid = vlow / getBaseBlockSize();
-							std::pair<uint64_t,uint64_t> const zoffset = getOffset(blockid,subblockid);
+							std::pair<uint64_t,uint64_t> const zoffset = data.getOffset(blockid,subblockid);
 
 							libmaus2::lz::SnappyInputStream::unique_ptr_type zptr(
 								new libmaus2::lz::SnappyInputStream(
@@ -367,29 +432,29 @@ namespace libmaus2
 					exp += V[i].second-V[i].first;
 				}
 
-				libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type> datastreams(info.size());
-				libmaus2::autoarray::AutoArray<libmaus2::lz::SnappyInputStream::unique_ptr_type> zdatastreams(size());
+				libmaus2::autoarray::AutoArray<libmaus2::aio::InputStreamInstance::unique_ptr_type> datastreams(data.info.size());
+				libmaus2::autoarray::AutoArray<libmaus2::lz::SnappyInputStream::unique_ptr_type> zdatastreams(data.size());
 				libmaus2::bambam::ReadEnds R;
 
-				for ( uint64_t i = 0; i < info.size(); ++i )
+				for ( uint64_t i = 0; i < data.info.size(); ++i )
 				{
 					// open data stream
 					libmaus2::aio::InputStreamInstance::unique_ptr_type tptr(
-						new libmaus2::aio::InputStreamInstance(info[i].datafilename)
+						new libmaus2::aio::InputStreamInstance(data.info[i].datafilename)
 					);
 					datastreams[i] = UNIQUE_PTR_MOVE(tptr);
 
 					// set up uncompressors
-					for ( uint64_t j = 0; j < info[i].indexoffset.size(); ++j )
+					for ( uint64_t j = 0; j < data.info[i].indexoffset.size(); ++j )
 					{
-						uint64_t const blockid    = O[i] + j;
+						uint64_t const blockid    = data.O[i] + j;
 						uint64_t const vlow = V[blockid].first;
 						uint64_t const vhigh = V[blockid].second;
 
 						if ( vlow < vhigh )
 						{
 							uint64_t const subblockid = vlow / getBaseBlockSize();
-							std::pair<uint64_t,uint64_t> const zoffset = getOffset(blockid,subblockid);
+							std::pair<uint64_t,uint64_t> const zoffset = data.getOffset(blockid,subblockid);
 
 							libmaus2::lz::SnappyInputStream::unique_ptr_type zptr(
 								new libmaus2::lz::SnappyInputStream(

src/libmaus2/bambam/parallel/BlockSortControl.hpp

@@ -420,6 +420,8 @@ namespace libmaus2
 
 				int verbose;
 
+				uint64_t const fragmergepar;
+
 				void freeBuffers()
 				{
 					fragmentBufferFreeListPreSort.reset();
@@ -466,6 +468,7 @@ namespace libmaus2
 					libmaus2::parallel::SimpleThreadPool & rSTP,
 					std::istream & in,
 					int const level,
+					uint64_t const rfragmergepar,
 					std::string const & rtempfileprefix,
 					std::string const & rhash,
 					bool const rfixmates = true,
@@ -546,7 +549,8 @@ namespace libmaus2
 					unmergeFragReadEndsRegions(0),
 					unmergePairReadEndsRegions(0),
 					hash(rhash),
-					verbose(0)
+					verbose(0),
+					fragmergepar(rfragmergepar)
 				{
 					STP.registerDispatcher(GICRPDid,&GICRPD);
 					STP.registerDispatcher(GIBDWPDid,&GIBDWPD);
@@ -1284,7 +1288,9 @@ namespace libmaus2
 					}
 				}
 
-				void enqueMergeFragReadEndsLists()
+				void enqueMergeFragReadEndsLists(
+					libmaus2::parallel::StdSemaphore::shared_ptr_type psem
+				)
 				{
 					if ( verbose )
 					{
@@ -1329,11 +1335,14 @@ namespace libmaus2
 						libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
 						std::cerr << "\t\t(enque FragReadEndsMergeWorkPackage)\n";
 					}
+					libmaus2::bambam::ReadEndsBlockIndexSetData::shared_ptr_type setData(
+						new libmaus2::bambam::ReadEndsBlockIndexSetData(*MI)
+					);
 					for ( uint64_t i = 0; i < SMI.size(); ++i )
 					{
 						ReadEndsMergeRequest req(Pdupbitvec.get(),MI,SMI[i]);
 						FragReadEndsMergeWorkPackage * package = fragReadEndsMergeWorkPackages.getPackage();
-						*package = FragReadEndsMergeWorkPackage(req,0/*prio*/,FREMWPDid);
+						*package = FragReadEndsMergeWorkPackage(req,setData,psem,0/*prio*/,FREMWPDid);
 						package->subid = i;
 						STP.enque(package);
 					}
@@ -1344,7 +1353,9 @@ namespace libmaus2
 					}
 				}
 
-				void enqueMergePairReadEndsLists()
+				void enqueMergePairReadEndsLists(
+					libmaus2::parallel::StdSemaphore::shared_ptr_type psem
+				)
 				{
 					if ( verbose )
 					{
@@ -1389,11 +1400,14 @@ namespace libmaus2
 						libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
 						std::cerr << "\t\t(enque PairReadEndsMergeWorkPackage)\n";
 					}
+					libmaus2::bambam::ReadEndsBlockIndexSetData::shared_ptr_type setData(
+						new libmaus2::bambam::ReadEndsBlockIndexSetData(*MI)
+					);
 					for ( uint64_t i = 0; i < SMI.size(); ++i )
 					{
 						ReadEndsMergeRequest req(Pdupbitvec.get(),MI,SMI[i]);
 						PairReadEndsMergeWorkPackage * package = pairReadEndsMergeWorkPackages.getPackage();
-						*package = PairReadEndsMergeWorkPackage(req,0/*prio*/,PREMWPDid);
+						*package = PairReadEndsMergeWorkPackage(req,setData,psem,0/*prio*/,PREMWPDid);
 						package->subid = i;
 						STP.enque(package);
 					}
@@ -1784,6 +1798,13 @@ namespace libmaus2
 
 				void mergeReadEndsLists(std::ostream & metricsstr, std::string const progname)
 				{
+					// set up semaphore to limit parallelism
+					libmaus2::parallel::StdSemaphore::shared_ptr_type psem(
+						new libmaus2::parallel::StdSemaphore
+					);
+					for ( uint64_t i = 0; i < fragmergepar; ++i )
+						psem->post();
+
 					// set up duplicate data structure
 					uint64_t const ureadsParsed = static_cast<uint64_t>(readsParsed);
 					libmaus2::bitio::BitVector::unique_ptr_type Tdupbitvec(new libmaus2::bitio::BitVector(ureadsParsed));
@@ -1797,7 +1818,7 @@ namespace libmaus2
 						libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
 						std::cerr << "\n\t(call enqueMergeFragReadEndsLists)\n";
 					}
-					enqueMergeFragReadEndsLists();
+					enqueMergeFragReadEndsLists(psem);
 					if ( verbose )
 					{
 						libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
@@ -1809,7 +1830,7 @@ namespace libmaus2
 						libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
 						std::cerr << "\t(call enqueMergePairReadEndsLists)\n";
 					}
-					enqueMergePairReadEndsLists();
+					enqueMergePairReadEndsLists(psem);
 					if ( verbose )
 					{
 						libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);

src/libmaus2/bambam/parallel/FragReadEndsMergeWorkPackage.hpp

@@ -21,6 +21,7 @@
 
 #include <libmaus2/parallel/SimpleThreadWorkPackage.hpp>
 #include <libmaus2/bambam/parallel/ReadEndsMergeRequest.hpp>
+#include <libmaus2/bambam/ReadEndsBlockIndexSet.hpp>
 
 namespace libmaus2
 {
@@ -35,6 +36,8 @@ namespace libmaus2
 				typedef libmaus2::util::shared_ptr<this_type>::type shared_ptr_type;
 
 				ReadEndsMergeRequest REQ;
+				libmaus2::bambam::ReadEndsBlockIndexSetData::shared_ptr_type setData;
+				libmaus2::parallel::StdSemaphore::shared_ptr_type psem;
 
 				FragReadEndsMergeWorkPackage() : libmaus2::parallel::SimpleThreadWorkPackage(), REQ()
 				{
@@ -42,11 +45,13 @@ namespace libmaus2
 				}
 				FragReadEndsMergeWorkPackage(
 					ReadEndsMergeRequest const & rREQ,
+					libmaus2::bambam::ReadEndsBlockIndexSetData::shared_ptr_type rsetData,
+					libmaus2::parallel::StdSemaphore::shared_ptr_type rpsem,
 					uint64_t const rpriority,
 					uint64_t const rdispatcherid,
 					uint64_t const rpackageid = 0
 				)
-				: libmaus2::parallel::SimpleThreadWorkPackage(rpriority,rdispatcherid,rpackageid), REQ(rREQ)
+				: libmaus2::parallel::SimpleThreadWorkPackage(rpriority,rdispatcherid,rpackageid), REQ(rREQ), setData(rsetData), psem(rpsem)
 				{
 
 				}
@@ -58,6 +63,8 @@ namespace libmaus2
 					{
 						libmaus2::parallel::SimpleThreadWorkPackage::operator=(O);
 						REQ = O.REQ;
+						setData = O.setData;
+						psem = O.psem;
 					}
 					return *this;
 				}

src/libmaus2/bambam/parallel/FragReadEndsMergeWorkPackageDispatcher.hpp

@@ -61,17 +61,23 @@ namespace libmaus2
 
 				virtual void dispatch(libmaus2::parallel::SimpleThreadWorkPackage * P, libmaus2::parallel::SimpleThreadPoolInterfaceEnqueTermInterface & /* tpi */)
 				{
+					FragReadEndsMergeWorkPackage * BP = NULL;
+					bool gotsem = false;
+
 					try
 					{
-						FragReadEndsMergeWorkPackage * BP = dynamic_cast<FragReadEndsMergeWorkPackage *>(P);
+						BP = dynamic_cast<FragReadEndsMergeWorkPackage *>(P);
 						assert ( BP );
 
+						BP->psem->wait();
+						gotsem = true;
+
 						if ( verbose )
 						{
 							libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
 							std::cerr << "FragReadEndsMergeWorkPackageDispatcher package " << P << " instantiating ReadEndsBlockIndexSet" << std::endl;
 						}
-						ReadEndsBlockIndexSet fragindexset(*(BP->REQ.MI));
+						ReadEndsBlockIndexSet fragindexset(*(BP->setData));
 						if ( verbose )
 						{
 							libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
@@ -119,6 +125,10 @@ namespace libmaus2
 						}
 
 						mergeFinishedInterface.fragReadEndsMergeWorkPackageFinished(BP);
+
+						BP->psem->post();
+						gotsem = false;
+
 						packageReturnInterface.fragReadEndsMergeWorkPackageReturn(BP);
 
 						if ( verbose )
@@ -129,6 +139,9 @@ namespace libmaus2
 					}
 					catch(std::exception const & ex)
 					{
+						if ( BP && gotsem )
+							BP->psem->post();
+
 						libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
 						std::cerr << "FragReadEndsMergeWorkPackageDispatcher package " << P << " exception: " << ex.what() << std::endl;
 						throw;

src/libmaus2/bambam/parallel/PairReadEndsMergeWorkPackage.hpp

@@ -21,6 +21,7 @@
 
 #include <libmaus2/bambam/parallel/ReadEndsMergeRequest.hpp>
 #include <libmaus2/parallel/SimpleThreadWorkPackage.hpp>
+#include <libmaus2/bambam/ReadEndsBlockIndexSet.hpp>
 
 namespace libmaus2
 {
@@ -35,18 +36,22 @@ namespace libmaus2
 				typedef libmaus2::util::shared_ptr<this_type>::type shared_ptr_type;
 
 				ReadEndsMergeRequest REQ;
+				libmaus2::bambam::ReadEndsBlockIndexSetData::shared_ptr_type setData;
+				libmaus2::parallel::StdSemaphore::shared_ptr_type psem;
 
-				PairReadEndsMergeWorkPackage() : libmaus2::parallel::SimpleThreadWorkPackage(), REQ()
+				PairReadEndsMergeWorkPackage() : libmaus2::parallel::SimpleThreadWorkPackage(), REQ(), setData()
 				{
 
 				}
 				PairReadEndsMergeWorkPackage(
 					ReadEndsMergeRequest const & rREQ,
+					libmaus2::bambam::ReadEndsBlockIndexSetData::shared_ptr_type rsetData,
+					libmaus2::parallel::StdSemaphore::shared_ptr_type rpsem,
 					uint64_t const rpriority,
 					uint64_t const rdispatcherid,
 					uint64_t const rpackageid = 0
 				)
-				: libmaus2::parallel::SimpleThreadWorkPackage(rpriority,rdispatcherid,rpackageid), REQ(rREQ)
+				: libmaus2::parallel::SimpleThreadWorkPackage(rpriority,rdispatcherid,rpackageid), REQ(rREQ), setData(rsetData), psem(rpsem)
 				{
 
 				}
@@ -58,6 +63,8 @@ namespace libmaus2
 					{
 						libmaus2::parallel::SimpleThreadWorkPackage::operator=(O);
 						REQ = O.REQ;
+						setData = O.setData;
+						psem = O.psem;
 					}
 					return *this;
 				}

src/libmaus2/bambam/parallel/PairReadEndsMergeWorkPackageDispatcher.hpp

@@ -64,17 +64,23 @@ namespace libmaus2
 
 				virtual void dispatch(libmaus2::parallel::SimpleThreadWorkPackage * P, libmaus2::parallel::SimpleThreadPoolInterfaceEnqueTermInterface & /* tpi */)
 				{
+					PairReadEndsMergeWorkPackage * BP = NULL;
+					bool gotsem = false;
+
 					try
 					{
-						PairReadEndsMergeWorkPackage * BP = dynamic_cast<PairReadEndsMergeWorkPackage *>(P);
+						BP = dynamic_cast<PairReadEndsMergeWorkPackage *>(P);
 						assert ( BP );
 
+						BP->psem->wait();
+						gotsem = true;
+
 						if ( verbose )
 						{
 							libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
 							std::cerr << "PairReadEndsMergeWorkPackageDispatcher package " << P << " instantiating ReadEndsBlockIndexSet" << std::endl;
 						}
-						ReadEndsBlockIndexSet pairindexset(*(BP->REQ.MI));
+						ReadEndsBlockIndexSet pairindexset(*(BP->setData));
 						if ( verbose )
 						{
 							libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
@@ -123,6 +129,10 @@ namespace libmaus2
 						}
 
 						mergeFinishedInterface.pairReadEndsMergeWorkPackageFinished(BP);
+
+						BP->psem->post();
+						gotsem = false;
+
 						packageReturnInterface.pairReadEndsMergeWorkPackageReturn(BP);
 
 						if ( verbose )
@@ -133,6 +143,9 @@ namespace libmaus2
 					}
 					catch(std::exception const & ex)
 					{
+						if ( BP && gotsem )
+							BP->psem->post();
+
 						libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
 						std::cerr << "PairReadEndsMergeWorkPackageDispatcher exception: " << ex.what() << std::endl;
 						throw;

src/libmaus2/network/ClientSocket.hpp

+/*
+    libmaus2
+    Copyright (C) 2009-2019 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_CLIENTSOCKET_HPP)
+#define LIBMAUS2_CLIENTSOCKET_HPP
+
+#include <libmaus2/network/SocketBase.hpp>
+
+namespace libmaus2
+{
+	namespace network
+	{
+		struct ClientSocket : public SocketBase
+		{
+			typedef ClientSocket this_type;
+			typedef ::libmaus2::util::unique_ptr<this_type>::type unique_ptr_type;
+
+			ClientSocket(unsigned short port, char const * hostname)
+			: SocketBase()
+			{
+				setAddress(hostname, remaddr);
+				remaddr.sin_port = htons(port);
+				remaddrset = true;
+
+				while ( ::connect(getFD(),reinterpret_cast<const sockaddr *>(&remaddr),sizeof(remaddr)) != 0 )
+				{
+					int const error = errno;
+
+					switch ( error )
+					{
+						case EINTR:
+						case EAGAIN:
+							break;
+						default:
+						{
+							::libmaus2::exception::LibMausException se;
+							se.getStream() << "ClientSocket: connect() failed with error " << strerror(error) << std::endl;
+							se.finish();
+							throw se;
+						}
+					}
+				}
+			}
+
+			static SocketBase::unique_ptr_type baseCast(ClientSocket::unique_ptr_type & C)
+			{
+				int const fd = C->getFD();
+				C->releaseFD();
+
+				try
+				{
+					SocketBase::unique_ptr_type ptr ( new SocketBase(fd) );
+					return ptr;
+				}
+				catch(...)
+				{
+					::close(fd);
+					throw;
+				}
+			}
+
+			static SocketBase::unique_ptr_type baseAlloc(unsigned short const port, char const * const hostname)
+			{
+				ClientSocket::unique_ptr_type ptr ( new ClientSocket(port,hostname) );
+				SocketBase::unique_ptr_type baseptr = baseCast(ptr);
+				return baseptr;
+			}
+
+			static SocketBase::unique_ptr_type baseAlloc(unsigned short const port, std::string const & hostname)
+			{
+				SocketBase::unique_ptr_type baseptr = baseAlloc(port,hostname.c_str());
+				return baseptr;
+			}
+		};
+	}
+}
+#endif