Commit 61eda99c authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 2.0.663

parent f9353a7e

ChangeLog

+39 −0
Original line number Diff line number Diff line 
libmaus2 (2.0.663-1) unstable; urgency=medium



  * allow registering files as temp files in SerialisingSortingBufferedOutputFileArray



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 27 Aug 2019 14:29:45 +0200



libmaus2 (2.0.662-1) unstable; urgency=medium



  * add ArrayErase specialisation for std::atomic



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 27 Aug 2019 09:31:33 +0200



libmaus2 (2.0.661-1) unstable; urgency=medium



  * fix broken handling of deletions in MD/NM calculation after adjusting interpretation of position field of BAM records

  * fix recalculateCigar function in BamAlignmentDecoderBase

  * fix doWrite function in PosixFdOutputStreamBuffer

  * change interpretation of BAM position such that it concerns the first reference base concerned (i.e. include deletions, do not skip to the first match/mismatch)



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 22 Aug 2019 08:24:12 +0200



libmaus2 (2.0.660-1) unstable; urgency=medium



  * implement storing of long names in FastAIndexGenerator



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 21 Aug 2019 09:17:02 +0200



libmaus2 (2.0.659-1) unstable; urgency=medium



  * fix number width in AlignmentPrint for large positions



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 20 Aug 2019 15:29:21 +0200



libmaus2 (2.0.658-1) unstable; urgency=medium



  * fix comparison with max value in KmerBase



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 20 Aug 2019 09:41:26 +0200



libmaus2 (2.0.657-1) unstable; urgency=medium



  * allow limiting parallelism in fragment merging of BlockSortControl (implicitely reduces number of open files)

autom4te.cache/output.0

+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 2.0.656.

@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.662.

@%:@

@%:@ Report bugs to <tischler@mpi-cbg.de>.

@%:@
@@ -590,8 +590,8 @@ MAKEFLAGS= 
# Identity of this package.

PACKAGE_NAME='libmaus2'

PACKAGE_TARNAME='libmaus2'

PACKAGE_VERSION='2.0.656'

PACKAGE_STRING='libmaus2 2.0.656'

PACKAGE_VERSION='2.0.662'

PACKAGE_STRING='libmaus2 2.0.662'

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 2.0.656 to adapt to many kinds of systems.









\`configure' configures libmaus2 2.0.662 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 2.0.656:";;









     short | recursive ) echo "Configuration of libmaus2 2.0.662:";;









   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 2.0.656









libmaus2 configure 2.0.662









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 2.0.656, which was









It was created by libmaus2 $as_me 2.0.662, 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=2:656:0









LIBRARY_VERSION=2:662:0









{ $as_echo "$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='2.0.656'









 VERSION='2.0.662'

























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 2.0.656, which was









This file was extended by libmaus2 $as_me 2.0.662, 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 2.0.656









libmaus2 config.status 2.0.662









configured by $0, generated by GNU Autoconf 2.69,









  with options \\"\$ac_cs_config\\"

































autom4te.cache/output.1



+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 2.0.657.









@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.663.









@%:@









@%:@ Report bugs to <tischler@mpi-cbg.de>.









@%:@ 








@@ -590,8 +590,8 @@ MAKEFLAGS=







# Identity of this package.









PACKAGE_NAME='libmaus2'









PACKAGE_TARNAME='libmaus2'









PACKAGE_VERSION='2.0.657'









PACKAGE_STRING='libmaus2 2.0.657'









PACKAGE_VERSION='2.0.663'









PACKAGE_STRING='libmaus2 2.0.663'









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 2.0.657 to adapt to many kinds of systems.









\`configure' configures libmaus2 2.0.663 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 2.0.657:";;









     short | recursive ) echo "Configuration of libmaus2 2.0.663:";;









   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 2.0.657









libmaus2 configure 2.0.663









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 2.0.657, which was









It was created by libmaus2 $as_me 2.0.663, 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=2:657:0









LIBRARY_VERSION=2:663:0









{ $as_echo "$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='2.0.657'









 VERSION='2.0.663'

























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 2.0.657, which was









This file was extended by libmaus2 $as_me 2.0.663, 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 2.0.657









libmaus2 config.status 2.0.663









configured by $0, generated by GNU Autoconf 2.69,









  with options \\"\$ac_cs_config\\"

































autom4te.cache/output.2



+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 2.0.657.









@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.663.









@%:@









@%:@ Report bugs to <tischler@mpi-cbg.de>.









@%:@ 








@@ -590,8 +590,8 @@ MAKEFLAGS=







# Identity of this package.









PACKAGE_NAME='libmaus2'









PACKAGE_TARNAME='libmaus2'









PACKAGE_VERSION='2.0.657'









PACKAGE_STRING='libmaus2 2.0.657'









PACKAGE_VERSION='2.0.663'









PACKAGE_STRING='libmaus2 2.0.663'









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 2.0.657 to adapt to many kinds of systems.









\`configure' configures libmaus2 2.0.663 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 2.0.657:";;









     short | recursive ) echo "Configuration of libmaus2 2.0.663:";;









   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 2.0.657









libmaus2 configure 2.0.663









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 2.0.657, which was









It was created by libmaus2 $as_me 2.0.663, 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=2:657:0









LIBRARY_VERSION=2:663:0









{ $as_echo "$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='2.0.657'









 VERSION='2.0.663'

























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 2.0.657, which was









This file was extended by libmaus2 $as_me 2.0.663, 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 2.0.657









libmaus2 config.status 2.0.663









configured by $0, generated by GNU Autoconf 2.69,









  with options \\"\$ac_cs_config\\"

































autom4te.cache/requests



+379
−379




























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