Commit f9353a7e authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.0.657

parent 59a4b494
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+26 −0
Original line number Diff line number Diff line
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
+11 −11
Original line number Diff line number Diff line
@%:@! /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 $0, generated by GNU Autoconf 2.69,
  with options \\"\$ac_cs_config\\"
+11 −11
Original line number Diff line number Diff line
@%:@! /bin/sh
@%:@ Guess values for system-dependent variables and create Makefiles.
@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.653.
@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.657.
@%:@
@%:@ Report bugs to <tischler@mpi-cbg.de>.
@%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='libmaus2'
PACKAGE_TARNAME='libmaus2'
PACKAGE_VERSION='2.0.653'
PACKAGE_STRING='libmaus2 2.0.653'
PACKAGE_VERSION='2.0.657'
PACKAGE_STRING='libmaus2 2.0.657'
PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1609,7 +1609,7 @@ if test "$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 $0, generated by GNU Autoconf 2.69,
  with options \\"\$ac_cs_config\\"
+11 −11
Original line number Diff line number Diff line
@%:@! /bin/sh
@%:@ Guess values for system-dependent variables and create Makefiles.
@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.653.
@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.657.
@%:@
@%:@ Report bugs to <tischler@mpi-cbg.de>.
@%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='libmaus2'
PACKAGE_TARNAME='libmaus2'
PACKAGE_VERSION='2.0.653'
PACKAGE_STRING='libmaus2 2.0.653'
PACKAGE_VERSION='2.0.657'
PACKAGE_STRING='libmaus2 2.0.657'
PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1609,7 +1609,7 @@ if test "$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\\"
+388 −388

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