ChangeLog

+libmaus2 (2.0.689-1) unstable; urgency=medium
+
+  * add isCoding,getStrand and getCDS in GTFData
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 20 Nov 2019 14:13:18 +0100
+
+libmaus2 (2.0.688-1) unstable; urgency=medium
+
+  * add get*Info in VCFParser
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 19 Nov 2019 13:53:41 +0100
+
+libmaus2 (2.0.687-1) unstable; urgency=medium
+
+  * update default sort block sizes in classes using serialised sorting
+  * add StreamGetObject in Makefile
+  * change default sort block size in SerialisingSortingBufferedOutputFile
+  * add test for SerialisingSortingBufferedOutputFile in testAIO
+  * reimplement SerialisingSortingBufferedOutput to use fixed size buffer
+  * add verbose mode for SerialisingMergingReadBack
+  * add verbose mode for SerialisingSortingBufferedOutputFile
+  * add lengthUTF8 in UTF8 class
+  * add CharArrayInputStream/CharArrayOutputStream/CountOutputStream/StreamGetObject plus tests
+  * add maxdepth field in ExonSubInfo
+  * add getStrings method in TabEntry
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 12 Nov 2019 17:19:33 +0100
+
+libmaus2 (2.0.686-1) unstable; urgency=medium
+
+  * add include statement for stdexcept in PosixFunctions.cpp
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 07 Nov 2019 11:04:53 +0100
+
+libmaus2 (2.0.685-1) unstable; urgency=medium
+
+  * add print method in GTFData/Gene/Transcript/Exon
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 07 Nov 2019 10:16:57 +0100
+
 libmaus2 (2.0.684-1) unstable; urgency=medium
 
   * add reset method in IndexBase

autom4te.cache/output.0

 @%:@! /bin/sh
 @%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.683.
+@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.688.
 @%:@
 @%:@ Report bugs to <tischler@mpi-cbg.de>.
 @%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libmaus2'
 PACKAGE_TARNAME='libmaus2'
-PACKAGE_VERSION='2.0.683'
-PACKAGE_STRING='libmaus2 2.0.683'
+PACKAGE_VERSION='2.0.688'
+PACKAGE_STRING='libmaus2 2.0.688'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1568,7 +1568,7 @@ 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 2.0.683 to adapt to many kinds of systems.
+\`configure' configures libmaus2 2.0.688 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1640,7 +1640,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libmaus2 2.0.683:";;
+     short | recursive ) echo "Configuration of libmaus2 2.0.688:";;
    esac
   cat <<\_ACEOF
@@ -1802,7 +1802,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libmaus2 configure 2.0.683
+libmaus2 configure 2.0.688
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2633,7 +2633,7 @@ 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 2.0.683, which was
+It was created by libmaus2 $as_me 2.0.688, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -2981,7 +2981,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
-LIBRARY_VERSION=2:683:0
+LIBRARY_VERSION=2:688:0
 { $as_echo "$as_me:${as_lineno-$LINENO}: Configuring for source in directory ${srcdir}" >&5
 $as_echo "$as_me: Configuring for source in directory ${srcdir}" >&6;}
 ac_aux_dir=
@@ -12537,7 +12537,7 @@ fi
 # Define the identity of the package.
  PACKAGE='libmaus2'
- VERSION='2.0.683'
+ VERSION='2.0.688'
 cat >>confdefs.h <<_ACEOF
@@ -26171,7 +26171,7 @@ cat >>$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 2.0.683, which was
+This file was extended by libmaus2 $as_me 2.0.688, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -26238,7 +26238,7 @@ _ACEOF
 cat >>$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 2.0.683
+libmaus2 config.status 2.0.688
 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 2.0.684.
+@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.689.
 @%:@
 @%:@ Report bugs to <tischler@mpi-cbg.de>.
 @%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libmaus2'
 PACKAGE_TARNAME='libmaus2'
-PACKAGE_VERSION='2.0.684'
-PACKAGE_STRING='libmaus2 2.0.684'
+PACKAGE_VERSION='2.0.689'
+PACKAGE_STRING='libmaus2 2.0.689'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1568,7 +1568,7 @@ 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 2.0.684 to adapt to many kinds of systems.
+\`configure' configures libmaus2 2.0.689 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1640,7 +1640,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libmaus2 2.0.684:";;
+     short | recursive ) echo "Configuration of libmaus2 2.0.689:";;
    esac
   cat <<\_ACEOF
@@ -1802,7 +1802,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libmaus2 configure 2.0.684
+libmaus2 configure 2.0.689
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2633,7 +2633,7 @@ 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 2.0.684, which was
+It was created by libmaus2 $as_me 2.0.689, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -2981,7 +2981,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
-LIBRARY_VERSION=2:684:0
+LIBRARY_VERSION=2:689:0
 { $as_echo "$as_me:${as_lineno-$LINENO}: Configuring for source in directory ${srcdir}" >&5
 $as_echo "$as_me: Configuring for source in directory ${srcdir}" >&6;}
 ac_aux_dir=
@@ -12537,7 +12537,7 @@ fi
 # Define the identity of the package.
  PACKAGE='libmaus2'
- VERSION='2.0.684'
+ VERSION='2.0.689'
 cat >>confdefs.h <<_ACEOF
@@ -26171,7 +26171,7 @@ cat >>$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 2.0.684, which was
+This file was extended by libmaus2 $as_me 2.0.689, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -26238,7 +26238,7 @@ _ACEOF
 cat >>$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 2.0.684
+libmaus2 config.status 2.0.689
 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 2.0.684.
+@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.689.
 @%:@
 @%:@ Report bugs to <tischler@mpi-cbg.de>.
 @%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libmaus2'
 PACKAGE_TARNAME='libmaus2'
-PACKAGE_VERSION='2.0.684'
-PACKAGE_STRING='libmaus2 2.0.684'
+PACKAGE_VERSION='2.0.689'
+PACKAGE_STRING='libmaus2 2.0.689'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1568,7 +1568,7 @@ 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 2.0.684 to adapt to many kinds of systems.
+\`configure' configures libmaus2 2.0.689 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1640,7 +1640,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libmaus2 2.0.684:";;
+     short | recursive ) echo "Configuration of libmaus2 2.0.689:";;
    esac
   cat <<\_ACEOF
@@ -1802,7 +1802,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libmaus2 configure 2.0.684
+libmaus2 configure 2.0.689
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2633,7 +2633,7 @@ 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 2.0.684, which was
+It was created by libmaus2 $as_me 2.0.689, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -2981,7 +2981,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
-LIBRARY_VERSION=2:684:0
+LIBRARY_VERSION=2:689:0
 { $as_echo "$as_me:${as_lineno-$LINENO}: Configuring for source in directory ${srcdir}" >&5
 $as_echo "$as_me: Configuring for source in directory ${srcdir}" >&6;}
 ac_aux_dir=
@@ -12537,7 +12537,7 @@ fi
 # Define the identity of the package.
  PACKAGE='libmaus2'
- VERSION='2.0.684'
+ VERSION='2.0.689'
 cat >>confdefs.h <<_ACEOF
@@ -26171,7 +26171,7 @@ cat >>$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 2.0.684, which was
+This file was extended by libmaus2 $as_me 2.0.689, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -26238,7 +26238,7 @@ _ACEOF
 cat >>$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 2.0.684
+libmaus2 config.status 2.0.689
 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], [2.0.684], [tischler@mpi-cbg.de], [libmaus2], [https://github.com/gt1/libmaus2])
+m4trace:configure.ac:1: -1- AC_INIT([libmaus2], [2.0.689], [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 2.0.684.
+# Generated by GNU Autoconf 2.69 for libmaus2 2.0.689.
 #
 # Report bugs to <tischler@mpi-cbg.de>.
 #
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libmaus2'
 PACKAGE_TARNAME='libmaus2'
-PACKAGE_VERSION='2.0.684'
-PACKAGE_STRING='libmaus2 2.0.684'
+PACKAGE_VERSION='2.0.689'
+PACKAGE_STRING='libmaus2 2.0.689'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1568,7 +1568,7 @@ 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 2.0.684 to adapt to many kinds of systems.
+\`configure' configures libmaus2 2.0.689 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1640,7 +1640,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libmaus2 2.0.684:";;
+     short | recursive ) echo "Configuration of libmaus2 2.0.689:";;
    esac
   cat <<\_ACEOF
@@ -1802,7 +1802,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libmaus2 configure 2.0.684
+libmaus2 configure 2.0.689
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2633,7 +2633,7 @@ 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 2.0.684, which was
+It was created by libmaus2 $as_me 2.0.689, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -2981,7 +2981,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
-LIBRARY_VERSION=2:684:0
+LIBRARY_VERSION=2:689:0
 { $as_echo "$as_me:${as_lineno-$LINENO}: Configuring for source in directory ${srcdir}" >&5
 $as_echo "$as_me: Configuring for source in directory ${srcdir}" >&6;}
 ac_aux_dir=
@@ -12537,7 +12537,7 @@ fi
 # Define the identity of the package.
  PACKAGE='libmaus2'
- VERSION='2.0.684'
+ VERSION='2.0.689'
 cat >>confdefs.h <<_ACEOF
@@ -26171,7 +26171,7 @@ cat >>$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 2.0.684, which was
+This file was extended by libmaus2 $as_me 2.0.689, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -26238,7 +26238,7 @@ _ACEOF
 cat >>$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 2.0.684
+libmaus2 config.status 2.0.689
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

configure.ac

-AC_INIT(libmaus2,2.0.684,[tischler@mpi-cbg.de],[libmaus2],[https://github.com/gt1/libmaus2])
-LIBRARY_VERSION=2:684:0
+AC_INIT(libmaus2,2.0.689,[tischler@mpi-cbg.de],[libmaus2],[https://github.com/gt1/libmaus2])
+LIBRARY_VERSION=2:689:0
 AC_MSG_NOTICE([Configuring for source in directory ${srcdir}])
 AC_CANONICAL_SYSTEM
 AC_CANONICAL_HOST

debian/changelog

+libmaus2 (2.0.689-1) unstable; urgency=medium
+
+  * New upstream version
+  * Set upstream metadata fields: Bug-Submit.
+
+ -- Andreas Tille <tille@debian.org>  Sun, 01 Dec 2019 08:48:47 +0100
+
 libmaus2 (2.0.684-1) unstable; urgency=medium
 
   * Team upload.

debian/upstream/metadata

 Registry:
- - Name: conda:bioconda
-   Entry: libmaus2
- - Name: OMICtools
-   Entry: NA
- - Name: bio.tools
-   Entry: libmaus
-   Comment: No refereral to a version 2
\ No newline at end of file
+- Name: conda:bioconda
+  Entry: libmaus2
+- Name: OMICtools
+  Entry: NA
+- Name: bio.tools
+  Entry: libmaus
+  Comment: No refereral to a version 2
+Bug-Submit: tischler@mpi-cbg.de

src/Makefile.am

@@ -1320,7 +1320,8 @@ libmaus2util_include_HEADERS=\
 	libmaus2/util/Base64.hpp \
 	libmaus2/util/AutoArrayUInt8TBaseAllocator.hpp \
 	libmaus2/util/AutoArrayUInt8TBaseTypeInfo.hpp \
-	libmaus2/util/DirectoryStructure.hpp
+	libmaus2/util/DirectoryStructure.hpp \
+	libmaus2/util/StreamGetObject.hpp
 
 libmaus2uint_includedir=$(includedir)/libmaus2/uint
 libmaus2uint_include_HEADERS=\
@@ -1439,8 +1440,14 @@ libmaus2aio_include_HEADERS=\
 	libmaus2/aio/MemoryBackedOutputStreamBuffer.hpp \
 	libmaus2/aio/MemoryBackedOutputStream.hpp \
 	libmaus2/aio/SkipConcatInputStream.hpp \
-	libmaus2/aio/SkipConcatInputStreamBuffer.hpp
-	
+	libmaus2/aio/SkipConcatInputStreamBuffer.hpp \
+	libmaus2/aio/CountOutputStreamBuffer.hpp \
+	libmaus2/aio/CountOutputStream.hpp \
+	libmaus2/aio/CharArrayInputStreamBuffer.hpp \
+	libmaus2/aio/CharArrayInputStream.hpp \
+	libmaus2/aio/CharArrayOutputStreamBuffer.hpp \
+	libmaus2/aio/CharArrayOutputStream.hpp
+
 libmaus2parallel_includedir=$(includedir)/libmaus2/parallel
 libmaus2parallel_include_HEADERS=\
 	libmaus2/parallel/StdThread.hpp \

src/Makefile.in

@@ -3692,7 +3692,8 @@ libmaus2util_include_HEADERS = \
 	libmaus2/util/Base64.hpp \
 	libmaus2/util/AutoArrayUInt8TBaseAllocator.hpp \
 	libmaus2/util/AutoArrayUInt8TBaseTypeInfo.hpp \
-	libmaus2/util/DirectoryStructure.hpp
+	libmaus2/util/DirectoryStructure.hpp \
+	libmaus2/util/StreamGetObject.hpp
 libmaus2uint_includedir = $(includedir)/libmaus2/uint
 libmaus2uint_include_HEADERS = \
@@ -3811,7 +3812,13 @@ libmaus2aio_include_HEADERS = \
 	libmaus2/aio/MemoryBackedOutputStreamBuffer.hpp \
 	libmaus2/aio/MemoryBackedOutputStream.hpp \
 	libmaus2/aio/SkipConcatInputStream.hpp \
-	libmaus2/aio/SkipConcatInputStreamBuffer.hpp
+	libmaus2/aio/SkipConcatInputStreamBuffer.hpp \
+	libmaus2/aio/CountOutputStreamBuffer.hpp \
+	libmaus2/aio/CountOutputStream.hpp \
+	libmaus2/aio/CharArrayInputStreamBuffer.hpp \
+	libmaus2/aio/CharArrayInputStream.hpp \
+	libmaus2/aio/CharArrayOutputStreamBuffer.hpp \
+	libmaus2/aio/CharArrayOutputStream.hpp
 libmaus2parallel_includedir = $(includedir)/libmaus2/parallel
 libmaus2parallel_include_HEADERS = \

src/libmaus2/aio/BufferedOutput.hpp

@@ -22,6 +22,14 @@
 
 #include <libmaus2/autoarray/AutoArray.hpp>
 #include <libmaus2/sorting/InPlaceParallelSort.hpp>
+#include <libmaus2/util/PutObject.hpp>
+#include <libmaus2/util/CountPutObject.hpp>
+#include <libmaus2/util/GetObject.hpp>
+#include <libmaus2/util/StreamGetObject.hpp>
+#include <libmaus2/aio/CountOutputStream.hpp>
+#include <libmaus2/aio/CharArrayInputStream.hpp>
+#include <libmaus2/aio/CharArrayOutputStream.hpp>
+#include <libmaus2/util/utf8.hpp>
 
 namespace libmaus2
 {
@@ -388,11 +396,219 @@ namespace libmaus2
 			}
 		};
 
+		template<typename _data_type, typename _order_type = std::less<_data_type> >
+		struct SerialisingBuffer
+		{
+			//! data type
+			typedef _data_type data_type;
+			//! order type
+			typedef _order_type order_type;
+			//!
+			typedef SerialisingBuffer<data_type,order_type> this_type;
+
+			std::ostream & out;
+			libmaus2::autoarray::AutoArray<char *> B;
+			order_type & order;
+
+			char ** pe;
+			char ** pc;
+
+			char * ca;
+			char * cc;
+
+			uint64_t w;
+
+			uint64_t threads;
+
+			/**
+			 * comparator class
+			 **/
+			struct Comparator
+			{
+				order_type * order;
+
+				Comparator(order_type & rorder)
+				: order(&rorder)
+				{
+
+				}
+
+				bool operator()(char * a, char * b) const
+				{
+					libmaus2::util::StreamGetObject<char const *> LA(a);
+					libmaus2::util::StreamGetObject<char const *> LB(b);
+
+					uint64_t const utfa = libmaus2::util::UTF8::decodeUTF8Unchecked(LA);
+					uint64_t const utfb = libmaus2::util::UTF8::decodeUTF8Unchecked(LB);
+
+					uint64_t const lutfa = libmaus2::util::UTF8::lengthUTF8(utfa);
+					uint64_t const lutfb = libmaus2::util::UTF8::lengthUTF8(utfb);
+
+					data_type A;
+					data_type B;
+					libmaus2::aio::CharArrayInputStream GA(a+lutfa,a+lutfa+utfa);
+					libmaus2::aio::CharArrayInputStream GB(b+lutfb,b+lutfb+utfb);
+
+					A.deserialise(GA);
+					B.deserialise(GB);
+
+					return (*order)(A,B);
+				}
+			};
+
+			Comparator comp;
+
+			/**
+			 * set up buffer for size
+			 **/
+			void setupBuffer(uint64_t const nbufsize)
+			{
+				uint64_t const abufsize = (nbufsize + sizeof(char *) - 1) / sizeof(char *);
+				B = libmaus2::autoarray::AutoArray<char *>();
+				B = libmaus2::autoarray::AutoArray<char *>(abufsize,false);
+
+				pe = B.end(),
+				pc = pe;
+
+				ca = reinterpret_cast<char *>(B.begin());
+				cc = ca;
+			}
+
+			/**
+			 * increase buffer size
+			 **/
+			void bumpBuffer()
+			{
+				uint64_t obufsize = B.size() * sizeof(char *);
+				setupBuffer(obufsize ? (2*obufsize) : 1);
+			}
+
+			SerialisingBuffer(
+				std::ostream & rout,
+				uint64_t const rbufsize,
+				order_type & rorder,
+				uint64_t const rthreads
+			) : out(rout), order(rorder), w(0), threads(rthreads), comp(order)
+			{
+				setupBuffer(rbufsize);
+			}
+
+			/**
+			 * flush buffer, return number of elements flushed and position of flushed block in output stream
+			 **/
+			std::pair<uint64_t,uint64_t> flush()
+			{
+				// number of bytes written before
+				uint64_t const pre_w = w;
+				// number of elements in buffer
+				uint64_t const n = pe-pc;
+
+				if ( threads <= 1 )
+					std::sort(pc,pc+n,comp);
+				else
+					libmaus2::sorting::InPlaceParallelSort::inplacesort2<
+						char **,Comparator
+					>(
+						pc,pc+n,
+						threads,
+						comp
+					);
+
+				// write sorted elements
+				data_type D;
+				for ( uint64_t i = 0; i < n; ++i )
+				{
+					// decode length of entry
+					libmaus2::util::StreamGetObject<char const *> LA(pc[i]);
+
+					uint64_t const utf = libmaus2::util::UTF8::decodeUTF8Unchecked(LA);
+					// get length of utf-8 code
+					uint64_t const lutf = libmaus2::util::UTF8::lengthUTF8(utf);
+
+					// set up stream for decoding object
+					libmaus2::aio::CharArrayInputStream GA(pc[i]+lutf,pc[i]+lutf+utf);
+
+					// decode object
+					D.deserialise(GA);
+					assert ( GA );
+
+					// encode object
+					D.serialise(out);
+
+					// add size of object
+					w += utf;
+				}
+
+				// reset buffer pointers
+				pc = pe;
+				cc = ca;
+
+				return std::pair<uint64_t,uint64_t>(n,pre_w);
+			}
+
+			/**
+			 * put one object, return number of flushed elements and file position of flush block
+			 **/
+			std::pair<uint64_t,uint64_t> put(data_type const & D)
+			{
+				// check size of object
+				libmaus2::aio::CountOutputStream CPO;
+				D.serialise(CPO);
+				CPO.flush();
+
+				// get length of object size in utf8
+				uint64_t const utfsize = libmaus2::util::UTF8::lengthUTF8(CPO.c);
+
+				// available space
+				uint64_t spaceav = reinterpret_cast<char const *>(pc) - cc;
+				// required space
+				uint64_t const spacereq = CPO.c + utfsize + sizeof(char *);
+
+				// empty flush info
+				std::pair<uint64_t,uint64_t> flushInfo(0,w);
+
+				// if space is insufficient
+				if ( spacereq > spaceav )
+				{
+					// flush buffer
+					flushInfo = flush();
+					// recompute free space
+					spaceav = reinterpret_cast<char const *>(pc) - cc;
+
+					// while buffer is too small to hold element
+					while ( spacereq > spaceav )
+					{
+						assert ( pc == pe );
+						assert ( cc == ca );
+						bumpBuffer();
+						spaceav = reinterpret_cast<char const *>(pc) - cc;
+					}
+				}
+
+				// output stream
+				libmaus2::aio::CharArrayOutputStream PO(cc,cc+utfsize+CPO.c);
+
+				// encode length as UTF-8
+				libmaus2::util::UTF8::encodeUTF8(CPO.c,PO);
+				// encode object
+				D.serialise(PO);
+
+				assert ( PO );
+
+				// store pointer
+				*--pc = cc;
+				// move data pointer
+				cc += CPO.c + utfsize;
+
+				return flushInfo;
+			}
+		};
+
 		/**
 		 * class for sorting buffer file output
 		 **/
 		template<typename _data_type, typename _order_type = std::less<_data_type> >
-		struct SerialisingSortingBufferedOutput : public BufferedOutputBase<_data_type>
+		struct SerialisingSortingBufferedOutput
 		{
 			//! data type
 			typedef _data_type data_type;
@@ -422,6 +638,7 @@ namespace libmaus2
 			order_type & order;
 			std::vector<BlockDescriptor> blocksizes;
 			uint64_t const numthreads;
+			SerialisingBuffer<data_type,order_type> B;
 
 			public:
 			/**
@@ -431,7 +648,7 @@ namespace libmaus2
 			 * @param bufsize size of buffer in elements
 			 **/
 			SerialisingSortingBufferedOutput(std::ostream & rout, uint64_t const bufsize, uint64_t const rnumthreads = 1)
-			: BufferedOutputBase<_data_type>(bufsize), out(rout), Porder(new order_type), order(*Porder), blocksizes(), numthreads(rnumthreads)
+			: out(rout), Porder(new order_type), order(*Porder), blocksizes(), numthreads(rnumthreads), B(out,bufsize,order,numthreads)
 			{
 
 			}
@@ -444,7 +661,7 @@ namespace libmaus2
 			 * @param rorder sort order
 			 **/
 			SerialisingSortingBufferedOutput(std::ostream & rout, uint64_t const bufsize, order_type & rorder, uint64_t const rnumthreads = 1)
-			: BufferedOutputBase<_data_type>(bufsize), out(rout), Porder(), order(rorder), blocksizes(), numthreads(rnumthreads)
+			: out(rout), Porder(), order(rorder), blocksizes(), numthreads(rnumthreads), B(out,bufsize,order,numthreads)
 			{
 
 			}
@@ -462,47 +679,18 @@ namespace libmaus2
 			 **/
 			void flush()
 			{
-				base_type::flush();
-				out.flush();
+				std::pair<uint64_t,uint64_t> const flushInfo = B.flush();
+
+				if ( flushInfo.first )
+					blocksizes.push_back(BlockDescriptor(flushInfo.first,flushInfo.second));
 			}
 
-			/**
-			 * write buffer to output stream
-			 **/
-			virtual void writeBuffer()
+			void put(data_type const & D)
 			{
-				if ( base_type::fill() )
-				{
-					if ( numthreads <= 1 )
-						std::sort(base_type::pa,base_type::pc,order);
-					else
-					{
-						libmaus2::sorting::InPlaceParallelSort::inplacesort2<data_type *,order_type>(
-							base_type::pa,base_type::pc,
-							numthreads,
-							order
-						);
-					}
-
-					uint64_t const fileptr = out.tellp();
+				std::pair<uint64_t,uint64_t> const flushInfo = B.put(D);
 
-					for ( data_type const * pi = base_type::pa; pi != base_type::pc; ++pi )
-					{
-						pi->serialise(out);
-
-						if ( ! out )
-						{
-							::libmaus2::exception::LibMausException se;
-							se.getStream() << "SerialisingSortingBufferedOutput: Failed to write" << std::endl;
-							se.finish();
-							throw se;
-						}
-					}
-
-					blocksizes.push_back(BlockDescriptor(base_type::fill(),fileptr));
-
-					base_type::reset();
-				}
+				if ( flushInfo.first )
+					blocksizes.push_back(BlockDescriptor(flushInfo.first,flushInfo.second));
 			}
 
 			/**

src/libmaus2/aio/CharArrayInputStream.hpp

+/*
+    libmaus2
+    Copyright (C) 2009-2014 German Tischler
+    Copyright (C) 2011-2014 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_AIO_CHARARRAYINPUTSTREAM_HPP)
+#define LIBMAUS2_AIO_CHARARRAYINPUTSTREAM_HPP
+
+#include <libmaus2/aio/CharArrayInputStreamBuffer.hpp>
+
+namespace libmaus2
+{
+	namespace aio
+	{
+		struct CharArrayInputStream : public CharArrayInputStreamBuffer, public std::istream
+		{
+			typedef CharArrayInputStream this_type;
+			typedef libmaus2::util::unique_ptr<this_type>::type unique_ptr_type;
+			typedef libmaus2::util::shared_ptr<this_type>::type shared_ptr_type;
+
+			CharArrayInputStream(char * ca, char * ce)
+			: CharArrayInputStreamBuffer(ca,ce), std::istream(this)
+			{}
+		};
+	}
+}
+#endif

src/libmaus2/aio/CharArrayInputStreamBuffer.hpp

+/*
+    libmaus2
+    Copyright (C) 2009-2014 German Tischler
+    Copyright (C) 2011-2014 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_AIO_CHARARRAYINPUTSTREAMBUFFER_HPP)
+#define LIBMAUS2_AIO_CHARARRAYINPUTSTREAMBUFFER_HPP
+
+#include <streambuf>
+#include <istream>
+#include <libmaus2/autoarray/AutoArray.hpp>
+
+namespace libmaus2
+{
+	namespace aio
+	{
+		struct CharArrayInputStreamBuffer : public ::std::streambuf
+		{
+			public:
+			typedef CharArrayInputStreamBuffer 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:
+			CharArrayInputStreamBuffer(CharArrayInputStreamBuffer const &);
+			CharArrayInputStreamBuffer & operator=(CharArrayInputStreamBuffer &);
+
+			public:
+			CharArrayInputStreamBuffer(
+				char * a,
+				char * e
+			)
+			{
+				setg(a,a,e);
+			}
+
+			private:
+			// gptr as unsigned pointer
+			uint8_t const * uptr() const
+			{
+				return reinterpret_cast<uint8_t const *>(gptr());
+			}
+
+			int_type underflow()
+			{
+				// if there is still data, then return it
+				if ( gptr() < egptr() )
+					return static_cast<int_type>(*uptr());
+
+				assert ( gptr() == egptr() );
+
+				return traits_type::eof();
+			}
+		};
+	}
+}
+#endif

src/libmaus2/aio/CharArrayOutputStream.hpp

+/*
+    libmaus2
+    Copyright (C) 2009-2014 German Tischler
+    Copyright (C) 2011-2014 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_AIO_CHARARRAYOUTPUTSTREAM_HPP)
+#define LIBMAUS2_AIO_CHARARRAYOUTPUTSTREAM_HPP
+
+#include <libmaus2/aio/CharArrayOutputStreamBuffer.hpp>
+
+namespace libmaus2
+{
+	namespace aio
+	{
+		struct CharArrayOutputStream : public CharArrayOutputStreamBuffer, public std::ostream
+		{
+			typedef CharArrayOutputStream this_type;
+			typedef libmaus2::util::unique_ptr<this_type>::type unique_ptr_type;
+			typedef libmaus2::util::shared_ptr<this_type>::type shared_ptr_type;
+
+			CharArrayOutputStream(char * ca, char * ce)
+			: CharArrayOutputStreamBuffer(ca,ce), std::ostream(this)
+			{}
+		};
+	}
+}
+#endif

src/libmaus2/aio/CharArrayOutputStreamBuffer.hpp

+/*
+    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_AIO_CHARARRAYOUTPUTSTREAMBUFFER_HPP)
+#define LIBMAUS2_AIO_CHARARRAYOUTPUTSTREAMBUFFER_HPP
+
+#include <ostream>
+#include <cmath>
+
+#include <libmaus2/LibMausConfig.hpp>
+
+namespace libmaus2
+{
+	namespace aio
+	{
+		struct CharArrayOutputStreamBuffer : public ::std::streambuf
+		{
+			char * a;
+			char * e;
+
+			public:
+			CharArrayOutputStreamBuffer(char * ra, char * re)
+			: a(ra), e(re)
+			{
+				setp(a,e);
+			}
+
+			int_type overflow(int_type /*c*/ = traits_type::eof())
+			{
+				return traits_type::eof();
+			}
+
+			int sync()
+			{
+				return 0; // no error, -1 for error
+			}
+		};
+	}
+}
+#endif

src/libmaus2/aio/CountOutputStream.hpp

+/*
+    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_AIO_COUNTOUTPUTSTREAM_HPP)
+#define LIBMAUS2_AIO_COUNTOUTPUTSTREAM_HPP
+
+#include <libmaus2/aio/CountOutputStreamBuffer.hpp>
+
+namespace libmaus2
+{
+	namespace aio
+	{
+		struct CountOutputStream : public CountOutputStreamBuffer, public std::ostream
+		{
+			typedef CountOutputStream this_type;
+			typedef libmaus2::util::unique_ptr<this_type>::type unique_ptr_type;
+			typedef libmaus2::util::shared_ptr<this_type>::type shared_ptr_type;
+
+			CountOutputStream()
+			: CountOutputStreamBuffer(), std::ostream(this)
+			{
+				exceptions(std::ios::badbit);
+			}
+			~CountOutputStream()
+			{
+				flush();
+			}
+		};
+	}
+}
+#endif

src/libmaus2/aio/CountOutputStreamBuffer.hpp

+/*
+    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_AIO_COUNTOUTPUTSTREAMBUFFER_HPP)
+#define LIBMAUS2_AIO_COUNTOUTPUTSTREAMBUFFER_HPP
+
+#include <ostream>
+#include <cmath>
+
+#include <libmaus2/LibMausConfig.hpp>
+
+namespace libmaus2
+{
+	namespace aio
+	{
+		struct CountOutputStreamBuffer : public ::std::streambuf
+		{
+			char B[16];
+			uint64_t c;
+
+			void doSync()
+			{
+				int64_t const n = pptr()-pbase();
+				pbump(-n);
+				c += n;
+			}
+
+			public:
+			CountOutputStreamBuffer()
+			: c(0)
+			{
+				setp(&B[0],&B[sizeof(B)]-1);
+			}
+
+			int_type overflow(int_type c = traits_type::eof())
+			{
+				if ( c != traits_type::eof() )
+				{
+					*pptr() = c;
+					pbump(1);
+					doSync();
+				}
+
+				return c;
+			}
+
+			int sync()
+			{
+				doSync();
+				return 0; // no error, -1 for error
+			}
+		};
+	}
+}
+#endif

src/libmaus2/aio/OutputStreamInstanceArray.hpp

@@ -73,10 +73,10 @@ namespace libmaus2
 
 			template<typename element_type>
 			void sortSingle(
-				uint64_t const blocksize = 1024ull,
-                                uint64_t const backblocksize = 1024ull,
-                                uint64_t const maxfan = 16ull,
-                                uint64_t const sortthreads = 1ull
+				uint64_t const blocksize = libmaus2::sorting::SerialisingSortingBufferedOutputFile<element_type>::getDefaultSortBlockSize(),
+                                uint64_t const backblocksize = libmaus2::sorting::SerialisingSortingBufferedOutputFile<element_type>::getDefaultBackBlockSize(),
+                                uint64_t const maxfan = libmaus2::sorting::SerialisingSortingBufferedOutputFile<element_type>::getDefaultMaxFan(),
+                                uint64_t const sortthreads = libmaus2::sorting::SerialisingSortingBufferedOutputFile<element_type>::getDefaultSortThreads()
 			)
 			{
 				flush();
@@ -89,10 +89,10 @@ namespace libmaus2
 			template<typename element_type>
 			void reduce(
 				std::string const & out,
-				uint64_t const blocksize = 1024ull,
-				uint64_t const backblocksize = 1024ull,
-				uint64_t const maxfan = 16ull,
-				uint64_t const sortthreads = 1ull
+				uint64_t const blocksize = libmaus2::sorting::SerialisingSortingBufferedOutputFile<element_type>::getDefaultSortBlockSize(),
+                                uint64_t const backblocksize = libmaus2::sorting::SerialisingSortingBufferedOutputFile<element_type>::getDefaultBackBlockSize(),
+                                uint64_t const maxfan = libmaus2::sorting::SerialisingSortingBufferedOutputFile<element_type>::getDefaultMaxFan(),
+                                uint64_t const sortthreads = libmaus2::sorting::SerialisingSortingBufferedOutputFile<element_type>::getDefaultSortThreads()
 			)
 			{
 				flush();