[med-svn] [Git][med-team/libmaus2][upstream] New upstream version 2.0.663
Steffen Möller
gitlab at salsa.debian.org
Wed Aug 28 16:11:02 BST 2019
Steffen Möller pushed to branch upstream at Debian Med / libmaus2
Commits:
61eda99c by Steffen Moeller at 2019-08-28T13:04:54Z
New upstream version 2.0.663
- - - - -
18 changed files:
- ChangeLog
- autom4te.cache/output.0
- autom4te.cache/output.1
- autom4te.cache/output.2
- autom4te.cache/requests
- autom4te.cache/traces.1
- configure
- configure.ac
- src/libmaus2/aio/PosixFdOutputStreamBuffer.hpp
- src/libmaus2/autoarray/AutoArray.hpp
- src/libmaus2/bambam/BamAlignment.hpp
- src/libmaus2/bambam/BamAlignmentDecoderBase.hpp
- src/libmaus2/bambam/MdNmRecalculation.hpp
- src/libmaus2/clustering/KmerBase.hpp
- src/libmaus2/fastx/FastAIndexGenerator.hpp
- src/libmaus2/lcs/AlignmentPrint.hpp
- src/libmaus2/sorting/SortingBufferedOutputFile.hpp
- src/test/testbamgetrefreg.cpp
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,42 @@
+libmaus2 (2.0.663-1) unstable; urgency=medium
+
+ * allow registering files as temp files in SerialisingSortingBufferedOutputFileArray
+
+ -- German Tischler-Höhle <germant at 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 at 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 at 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 at 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 at 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 at 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
=====================================
@@ -1,6 +1,6 @@
@%:@! /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 at 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 at 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 $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
=====================================
autom4te.cache/output.1
=====================================
@@ -1,6 +1,6 @@
@%:@! /bin/sh
@%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.657.
+@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.663.
@%:@
@%:@ Report bugs to <tischler at mpi-cbg.de>.
@%:@
@@ -590,8 +590,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='libmaus2'
PACKAGE_TARNAME='libmaus2'
-PACKAGE_VERSION='2.0.657'
-PACKAGE_STRING='libmaus2 2.0.657'
+PACKAGE_VERSION='2.0.663'
+PACKAGE_STRING='libmaus2 2.0.663'
PACKAGE_BUGREPORT='tischler at mpi-cbg.de'
PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1609,7 +1609,7 @@ if test "$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 $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
=====================================
autom4te.cache/output.2
=====================================
@@ -1,6 +1,6 @@
@%:@! /bin/sh
@%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.657.
+@%:@ Generated by GNU Autoconf 2.69 for libmaus2 2.0.663.
@%:@
@%:@ Report bugs to <tischler at mpi-cbg.de>.
@%:@
@@ -590,8 +590,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='libmaus2'
PACKAGE_TARNAME='libmaus2'
-PACKAGE_VERSION='2.0.657'
-PACKAGE_STRING='libmaus2 2.0.657'
+PACKAGE_VERSION='2.0.663'
+PACKAGE_STRING='libmaus2 2.0.663'
PACKAGE_BUGREPORT='tischler at mpi-cbg.de'
PACKAGE_URL='https://github.com/gt1/libmaus2'
@@ -1609,7 +1609,7 @@ if test "$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
=====================================
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- 'AC_LIBTOOL_SYS_MAX_CMD_LEN' => 1,
- 'LTDL_INSTALLABLE' => 1
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+ 'LT_FUNC_DLSYM_USCORE' => 1,
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}
], 'Autom4te::Request' ),
bless( [
@@ -250,66 +250,66 @@
'configure.ac'
],
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+ 'AC_CONFIG_SUBDIRS' => 1
}
], 'Autom4te::Request' ),
bless( [
@@ -353,198 +353,198 @@
'configure.ac'
],
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+ '_LT_PROG_CXX' => 1,
'AC_LTDL_SYS_DLOPEN_DEPLIBS' => 1,
- 'AM_INIT_AUTOMAKE' => 1,
- 'AC_PATH_TOOL_PREFIX' => 1,
- '_LT_AC_LANG_F77' => 1,
- 'AC_LTDL_PREOPEN' => 1,
- 'LTDL_CONVENIENCE' => 1,
+ 'AM_PROG_NM' => 1,
+ 'AC_ENABLE_STATIC' => 1,
+ 'AC_LTDL_SYSSEARCHPATH' => 1,
+ '_LT_PROG_LTMAIN' => 1,
'AM_PROG_LD' => 1,
- 'm4_pattern_allow' => 1,
- 'AC_DISABLE_FAST_INSTALL' => 1,
- '_m4_warn' => 1,
- '_AM_SET_OPTIONS' => 1,
- 'AC_LIBTOOL_LANG_C_CONFIG' => 1,
- 'LT_PROG_GO' => 1,
- '_LTDL_SETUP' => 1,
- '_AM_SUBST_NOTMAKE' => 1,
- 'AC_LTDL_DLLIB' => 1,
- 'LT_CONFIG_LTDL_DIR' => 1,
+ '_LT_WITH_SYSROOT' => 1,
'AM_AUTOMAKE_VERSION' => 1,
- 'LT_SYS_DLOPEN_DEPLIBS' => 1,
- '_LT_PATH_TOOL_PREFIX' => 1,
- 'm4_pattern_forbid' => 1,
- 'AM_DEP_TRACK' => 1,
- 'AC_LIBTOOL_SETUP' => 1,
- 'LT_OUTPUT' => 1,
- 'AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE' => 1,
- 'LT_AC_PROG_EGREP' => 1,
- 'AU_DEFUN' => 1,
- 'AC_LIBTOOL_LANG_GCJ_CONFIG' => 1,
- '_LT_LINKER_BOILERPLATE' => 1,
+ '_LT_AC_PROG_ECHO_BACKSLASH' => 1,
+ '_AC_PROG_LIBTOOL' => 1,
+ 'PKG_INSTALLDIR' => 1,
+ 'AC_LIBTOOL_F77' => 1,
+ 'AC_LTDL_DLLIB' => 1,
+ 'AC_CONFIG_MACRO_DIR' => 1,
+ 'LT_PROG_GO' => 1,
+ 'LT_PROG_RC' => 1,
+ 'AC_LTDL_SHLIBEXT' => 1,
+ 'LT_SYS_MODULE_EXT' => 1,
+ 'AC_LIBTOOL_SYS_MAX_CMD_LEN' => 1,
+ 'AC_LTDL_PREOPEN' => 1,
+ 'AM_PROG_INSTALL_STRIP' => 1,
+ 'AM_OUTPUT_DEPENDENCY_COMMANDS' => 1,
'_LT_AC_PROG_CXXCPP' => 1,
- 'LT_AC_PROG_GCJ' => 1,
- 'LT_SYS_MODULE_PATH' => 1,
+ '_AC_AM_CONFIG_HEADER_HOOK' => 1,
'_AM_CONFIG_MACRO_DIRS' => 1,
+ 'AC_DEFUN_ONCE' => 1,
'AC_CONFIG_MACRO_DIR_TRACE' => 1,
- '_LT_PROG_F77' => 1,
- 'AC_LIBTOOL_PICMODE' => 1,
- 'AC_LTDL_ENABLE_INSTALL' => 1,
+ 'LT_SYS_SYMBOL_USCORE' => 1,
+ '_AM_SUBST_NOTMAKE' => 1,
+ '_LT_AC_LOCK' => 1,
+ 'AC_LIBTOOL_GCJ' => 1,
+ 'AM_PROG_CC_C_O' => 1,
+ 'AC_LTDL_OBJDIR' => 1,
+ 'LTDL_CONVENIENCE' => 1,
'AC_LIBTOOL_LINKER_OPTION' => 1,
- 'LT_PATH_NM' => 1,
- 'AM_MAKE_INCLUDE' => 1,
- 'AC_LIBTOOL_CONFIG' => 1,
- 'AC_LIBTOOL_DLOPEN_SELF' => 1,
+ '_LTDL_SETUP' => 1,
+ 'LT_LIB_M' => 1,
+ '_LT_AC_TAGCONFIG' => 1,
+ '_LT_LIBOBJ' => 1,
+ 'LTOPTIONS_VERSION' => 1,
+ '_PKG_SHORT_ERRORS_SUPPORTED' => 1,
+ 'LT_CMD_MAX_LEN' => 1,
+ '_AM_IF_OPTION' => 1,
'AC_LIBTOOL_SYS_HARD_LINK_LOCKS' => 1,
- '_AM_PROG_CC_C_O' => 1,
- 'LTDL_INSTALLABLE' => 1,
- 'AC_LIBTOOL_SYS_MAX_CMD_LEN' => 1,
- 'AM_SET_LEADING_DOT' => 1,
- 'AM_PROG_INSTALL_SH' => 1,
- '_AM_MANGLE_OPTION' => 1,
- 'PKG_NOARCH_INSTALLDIR' => 1,
- '_LT_AC_SYS_LIBPATH_AIX' => 1,
- 'AC_LIBTOOL_OBJDIR' => 1,
+ '_AM_DEPENDENCIES' => 1,
+ 'AM_MISSING_HAS_RUN' => 1,
'AM_DISABLE_STATIC' => 1,
- '_LT_COMPILER_BOILERPLATE' => 1,
- 'LT_AC_PROG_RC' => 1,
- 'AC_DEFUN' => 1,
- '_LT_PROG_LTMAIN' => 1,
- 'AM_SET_CURRENT_AUTOMAKE_VERSION' => 1,
- 'AC_ENABLE_SHARED' => 1,
- '_LT_AC_TRY_DLOPEN_SELF' => 1
+ 'm4_pattern_allow' => 1,
+ '_LT_AC_TRY_DLOPEN_SELF' => 1,
+ 'AC_LIBTOOL_CXX' => 1,
+ '_AM_OUTPUT_DEPENDENCY_COMMANDS' => 1,
+ 'AC_LIBTOOL_PICMODE' => 1,
+ '_LT_COMPILER_BOILERPLATE' => 1
}
], 'Autom4te::Request' )
);
=====================================
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], [2.0.657], [tischler at mpi-cbg.de], [libmaus2], [https://github.com/gt1/libmaus2])
+m4trace:configure.ac:1: -1- AC_INIT([libmaus2], [2.0.663], [tischler at 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
=====================================
@@ -1,6 +1,6 @@
#! /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 at 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 at 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\\"
=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
-AC_INIT(libmaus2,2.0.657,[tischler at mpi-cbg.de],[libmaus2],[https://github.com/gt1/libmaus2])
-LIBRARY_VERSION=2:657:0
+AC_INIT(libmaus2,2.0.663,[tischler at mpi-cbg.de],[libmaus2],[https://github.com/gt1/libmaus2])
+LIBRARY_VERSION=2:663:0
AC_MSG_NOTICE([Configuring for source in directory ${srcdir}])
AC_CANONICAL_SYSTEM
AC_CANONICAL_HOST
=====================================
src/libmaus2/aio/PosixFdOutputStreamBuffer.hpp
=====================================
@@ -251,6 +251,7 @@ namespace libmaus2
assert ( w <= static_cast<int64_t>(n) );
n -= w;
writepos += w;
+ p += w;
}
}
}
=====================================
src/libmaus2/autoarray/AutoArray.hpp
=====================================
@@ -410,6 +410,20 @@ namespace libmaus2
static void erase(std::unique_ptr<N> * array, uint64_t const n);
};
+ /**
+ * class for erasing an array of std::atomic objects
+ **/
+ template<typename N>
+ struct ArrayErase< std::atomic<N> >
+ {
+ /**
+ * erase an array of n elements of type std::atomic<N>
+ * @param array to be erased
+ * @param n number of elements in array
+ **/
+ static void erase(std::atomic<N> * array, uint64_t const n);
+ };
+
template<typename N, alloc_type atype>
struct AutoArrayAllocate
{
@@ -1890,6 +1904,13 @@ namespace libmaus2
array[i] = UNIQUE_PTR_MOVE(std::unique_ptr<N>());
}
+ template<typename N>
+ void ArrayErase< std::atomic<N> >::erase(std::atomic<N> * array, uint64_t const n)
+ {
+ for ( uint64_t i = 0; i < n; ++i )
+ std::atomic_init(&array[i],N());
+ }
+
template<typename N, alloc_type atype>
bool operator==(AutoArray<N,atype> const & A, AutoArray<N,atype> const & B)
{
=====================================
src/libmaus2/bambam/BamAlignment.hpp
=====================================
@@ -472,7 +472,7 @@ namespace libmaus2
{
if ( isMapped() )
{
- it += getPos() - getFrontDel();
+ it += getPos();
std::string const R = getRead();
std::string::const_iterator itr = R.begin();
@@ -1837,7 +1837,7 @@ namespace libmaus2
return libmaus2::math::IntegerInterval<int64_t>::empty();
else
{
- int64_t const start = getPos() - getFrontDel();
+ int64_t const start = getPos();
int64_t const end = start + getReferenceLength();
return libmaus2::math::IntegerInterval<int64_t>(start,end-1);
}
@@ -2375,11 +2375,11 @@ namespace libmaus2
}
/**
- * @return getPos() - getFrontDel()
+ * @return getPos()
**/
int64_t getRefStart() const
{
- return getPos() - getFrontDel();
+ return getPos();
}
/**
@@ -3017,7 +3017,7 @@ namespace libmaus2
if ( ! reflen )
return libmaus2::math::IntegerInterval<int64_t>::empty();
- int64_t const start = getNextPos() - getNextFrontDel(Aop);
+ int64_t const start = getNextPos();
int64_t const end = start + reflen;
return libmaus2::math::IntegerInterval<int64_t>(start,end-1);
}
=====================================
src/libmaus2/bambam/BamAlignmentDecoderBase.hpp
=====================================
@@ -4534,7 +4534,7 @@ namespace libmaus2
{
true, // LIBMAUS2_BAMBAM_CMATCH = 0,
false, // LIBMAUS2_BAMBAM_CINS = 1,
- false, // LIBMAUS2_BAMBAM_CDEL = 2,
+ true, // LIBMAUS2_BAMBAM_CDEL = 2,
false, // LIBMAUS2_BAMBAM_CREF_SKIP = 3,
false, // LIBMAUS2_BAMBAM_CSOFT_CLIP = 4,
false, // LIBMAUS2_BAMBAM_CHARD_CLIP = 5,
@@ -4670,7 +4670,7 @@ namespace libmaus2
{
true, // LIBMAUS2_BAMBAM_CMATCH = 0,
false, // LIBMAUS2_BAMBAM_CINS = 1,
- false, // LIBMAUS2_BAMBAM_CDEL = 2,
+ true, // LIBMAUS2_BAMBAM_CDEL = 2,
false, // LIBMAUS2_BAMBAM_CREF_SKIP = 3,
false, // LIBMAUS2_BAMBAM_CSOFT_CLIP = 4,
false, // LIBMAUS2_BAMBAM_CHARD_CLIP = 5,
@@ -4805,7 +4805,7 @@ namespace libmaus2
{
true, // LIBMAUS2_BAMBAM_CMATCH = 0,
false, // LIBMAUS2_BAMBAM_CINS = 1,
- false, // LIBMAUS2_BAMBAM_CDEL = 2,
+ true, // LIBMAUS2_BAMBAM_CDEL = 2,
false, // LIBMAUS2_BAMBAM_CREF_SKIP = 3,
false, // LIBMAUS2_BAMBAM_CSOFT_CLIP = 4,
false, // LIBMAUS2_BAMBAM_CHARD_CLIP = 5,
@@ -4919,7 +4919,7 @@ namespace libmaus2
}
assert ( readpos == getLseq(B) );
- assert ( refpos == static_cast<int64_t>(getPos(B)) + static_cast<int64_t>(getReferenceAdvance(B)) );
+ assert ( refpos == static_cast<int64_t>(getPos(B)) + static_cast<int64_t>(getReferenceLength(B)) );
if ( Vout.size() > cigopin.size() )
cigopin.resize(Vout.size());
@@ -4952,7 +4952,7 @@ namespace libmaus2
std::ostream * errstr = &std::cerr
)
{
- static const bool calmd_preterm[] =
+ static const bool calmd_matchop[] =
{
true, // LIBMAUS2_BAMBAM_CMATCH = 0,
false, // LIBMAUS2_BAMBAM_CINS = 1,
@@ -5040,7 +5040,7 @@ namespace libmaus2
int32_t const cigo = cigop[cigi].first;
uint64_t const cigp = cigop[cigi].second;
- if ( calmd_preterm[cigo] )
+ if ( calmd_matchop[cigo] )
{
uint64_t l = 0;
while ( l != cigp )
@@ -5191,7 +5191,7 @@ namespace libmaus2
{
true, // LIBMAUS2_BAMBAM_CMATCH = 0,
false, // LIBMAUS2_BAMBAM_CINS = 1,
- false, // LIBMAUS2_BAMBAM_CDEL = 2,
+ true, // LIBMAUS2_BAMBAM_CDEL = 2,
false, // LIBMAUS2_BAMBAM_CREF_SKIP = 3,
false, // LIBMAUS2_BAMBAM_CSOFT_CLIP = 4,
false, // LIBMAUS2_BAMBAM_CHARD_CLIP = 5,
=====================================
src/libmaus2/bambam/MdNmRecalculation.hpp
=====================================
@@ -340,8 +340,7 @@ namespace libmaus2
{
int64_t const refid = libmaus2::bambam::BamAlignmentDecoderBase::getRefID(D);
int64_t const pos =
- libmaus2::bambam::BamAlignmentDecoderBase::getPos(D) -
- libmaus2::bambam::BamAlignmentDecoderBase::getFrontDel(D)
+ libmaus2::bambam::BamAlignmentDecoderBase::getPos(D)
;
int64_t const refend = pos + libmaus2::bambam::BamAlignmentDecoderBase::getReferenceLength(D);
std::string const & ref = loadReference(refid);
=====================================
src/libmaus2/clustering/KmerBase.hpp
=====================================
@@ -89,12 +89,12 @@ namespace libmaus2
if ( fword <= rword )
{
- if ( (fword>>hashshift) >= minhash && (fword>>hashshift) < maxhash )
+ if ( (fword>>hashshift) >= minhash && (fword>>hashshift) <= maxhash )
callback(fword);
}
else
{
- if ( (rword>>hashshift) >= minhash && (rword>>hashshift) < maxhash )
+ if ( (rword>>hashshift) >= minhash && (rword>>hashshift) <= maxhash )
callback(rword);
}
}
@@ -165,12 +165,12 @@ namespace libmaus2
if ( fword <= rword )
{
- if ( (fword>>hashshift) >= minhash && (fword>>hashshift) < maxhash )
+ if ( (fword>>hashshift) >= minhash && (fword>>hashshift) <= maxhash )
callback(fword,z,false);
}
else
{
- if ( (rword>>hashshift) >= minhash && (rword>>hashshift) < maxhash )
+ if ( (rword>>hashshift) >= minhash && (rword>>hashshift) <= maxhash )
callback(rword,z,true);
}
}
@@ -240,12 +240,12 @@ namespace libmaus2
if ( fword <= rword )
{
- if ( (fword>>hashshift) >= minhash && (fword>>hashshift) < maxhash )
+ if ( (fword>>hashshift) >= minhash && (fword>>hashshift) <= maxhash )
callback(fword,z,false);
}
else
{
- if ( (rword>>hashshift) >= minhash && (rword>>hashshift) < maxhash )
+ if ( (rword>>hashshift) >= minhash && (rword>>hashshift) <= maxhash )
callback(rword,z,true);
}
}
@@ -308,7 +308,7 @@ namespace libmaus2
{
uint64_t const fword = forw.buffer;
- if ( (fword>>hashshift) >= minhash && (fword>>hashshift) < maxhash )
+ if ( (fword>>hashshift) >= minhash && (fword>>hashshift) <= maxhash )
callback(fword,z);
}
@@ -365,7 +365,7 @@ namespace libmaus2
{
uint64_t const fword = forw.buffer;
- if ( (fword>>hashshift) >= minhash && (fword>>hashshift) < maxhash )
+ if ( (fword>>hashshift) >= minhash && (fword>>hashshift) <= maxhash )
callback(fword,z);
}
@@ -430,7 +430,7 @@ namespace libmaus2
{
uint64_t const fword = forw.buffer;
- if ( (fword>>hashshift) >= minhash && (fword>>hashshift) < maxhash )
+ if ( (fword>>hashshift) >= minhash && (fword>>hashshift) <= maxhash )
callback(fword,-static_cast<int>(z)-1);
}
}
@@ -479,7 +479,7 @@ namespace libmaus2
{
uint64_t const fword = forw.buffer;
- if ( (fword>>hashshift) >= minhash && (fword>>hashshift) < maxhash )
+ if ( (fword>>hashshift) >= minhash && (fword>>hashshift) <= maxhash )
callback(fword,z);
}
=====================================
src/libmaus2/fastx/FastAIndexGenerator.hpp
=====================================
@@ -1,6 +1,6 @@
/*
libmaus2
- Copyright (C) 2016 German Tischler
+ Copyright (C) 2016-2019 German Tischler-Höhle
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
@@ -20,10 +20,13 @@
#include <libmaus2/aio/InputStreamInstance.hpp>
#include <libmaus2/aio/OutputStreamInstance.hpp>
+#include <libmaus2/aio/OutputStreamFactoryContainer.hpp>
#include <libmaus2/fastx/FastAIndex.hpp>
#include <libmaus2/fastx/SpaceTable.hpp>
+#include <libmaus2/util/ArgInfo.hpp>
#include <libmaus2/util/GetFileSize.hpp>
#include <libmaus2/util/LineBuffer.hpp>
+#include <libmaus2/util/TempFileRemovalContainer.hpp>
namespace libmaus2
{
@@ -31,22 +34,61 @@ namespace libmaus2
{
struct FastAIndexGenerator
{
- static void generate(std::string const & fastaname, std::string const & fainame, int const verbose)
+ static bool needRun(
+ std::string const & fastaname, std::string const & fainame, std::string const * plongnamefn
+ )
{
if ( (! libmaus2::util::GetFileSize::fileExists(fainame)) || (libmaus2::util::GetFileSize::isOlder(fainame,fastaname) ) )
+ return true;
+
+ if ( plongnamefn )
+ {
+ std::string const & longnamefn = *plongnamefn;
+
+ if ( (! libmaus2::util::GetFileSize::fileExists(longnamefn)) || (libmaus2::util::GetFileSize::isOlder(longnamefn,fastaname) ) )
+ return true;
+ }
+
+ return false;
+ }
+
+ static void generate(
+ std::string const & fastaname,
+ std::string const & fainame,
+ int const verbose,
+ std::string const * plongnamefn = NULL,
+ std::string const * ptmpprefix = NULL
+ )
+ {
+ if ( needRun(fastaname,fainame,plongnamefn) )
{
if ( verbose > 0 )
std::cerr << "[V] generating " << fainame << "...";
+ std::string const tmpprefix = ptmpprefix ? (*ptmpprefix) : libmaus2::util::ArgInfo::getDefaultTmpFileName(fainame);
+
+ std::string const fainametmp = tmpprefix + ".faitmp";
+ libmaus2::util::TempFileRemovalContainer::addTempFile(fainametmp);
+ std::string const longnametmp = tmpprefix + ".longnametmp";
+ libmaus2::util::TempFileRemovalContainer::addTempFile(longnametmp);
+
libmaus2::aio::InputStreamInstance ISI(fastaname);
- libmaus2::aio::OutputStreamInstance OSI(fainame);
+ libmaus2::aio::OutputStreamInstance::unique_ptr_type OSI(new libmaus2::aio::OutputStreamInstance(fainametmp));
libmaus2::util::LineBuffer LB(ISI, 8*1024);
libmaus2::fastx::SpaceTable ST;
+ libmaus2::aio::OutputStreamInstance::unique_ptr_type longOSI;
+ if ( plongnamefn )
+ {
+ libmaus2::aio::OutputStreamInstance::unique_ptr_type tOSI(new libmaus2::aio::OutputStreamInstance(longnametmp));
+ longOSI = UNIQUE_PTR_MOVE(tOSI);
+ }
+
char const * a = 0;
char const * e = 0;
std::string seqname;
+ std::string longname;
int64_t linewidth = -1;
int64_t linelength = -1;
uint64_t seqlength = 0;
@@ -58,9 +100,14 @@ namespace libmaus2
if ( e-a && *a == '>' )
{
if ( seqname.size() )
- OSI << seqname << "\t" << seqlength << "\t" << seqoffset << "\t" << linewidth << "\t" << linelength << std::endl;
+ {
+ (*OSI) << seqname << "\t" << seqlength << "\t" << seqoffset << "\t" << linewidth << "\t" << linelength << "\n";
+ if ( longOSI )
+ *longOSI << longname << "\n";
+ }
- seqname = libmaus2::fastx::FastAIndex::computeShortName(std::string(a+1,e));
+ longname = std::string(a+1,e);
+ seqname = libmaus2::fastx::FastAIndex::computeShortName(longname);
linewidth = -1;
linelength = -1;
seqlength = 0;
@@ -89,7 +136,50 @@ namespace libmaus2
o += (e-a)+1;
}
if ( seqname.size() )
- OSI << seqname << "\t" << seqlength << "\t" << seqoffset << "\t" << linewidth << "\t" << linelength << std::endl;
+ {
+ (*OSI) << seqname << "\t" << seqlength << "\t" << seqoffset << "\t" << linewidth << "\t" << linelength << "\n";
+ if ( longOSI )
+ *longOSI << longname << "\n";
+ }
+
+ OSI->flush();
+
+ if ( ! *OSI )
+ {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] FastAIndexGenerator::generate: unable to write output" << std::endl;
+ lme.finish();
+ throw lme;
+ }
+
+ OSI.reset();
+
+ libmaus2::aio::OutputStreamFactoryContainer::rename(
+ fainametmp,
+ fainame
+ );
+
+ if ( longOSI )
+ {
+ longOSI->flush();
+
+ if ( ! *longOSI )
+ {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] FastAIndexGenerator::generate: unable to write output" << std::endl;
+ lme.finish();
+ throw lme;
+ }
+
+ longOSI.reset();
+
+ assert ( plongnamefn );
+ libmaus2::aio::OutputStreamFactoryContainer::rename(
+ longnametmp,
+ *plongnamefn
+ );
+ }
+
if ( verbose > 0 )
std::cerr << "done." << std::endl;
=====================================
src/libmaus2/lcs/AlignmentPrint.hpp
=====================================
@@ -21,6 +21,7 @@
#define LIBMAUS2_LCS_ALIGNMENTPRINT_HPP
#include <libmaus2/lcs/BaseConstants.hpp>
+#include <libmaus2/util/NumberSerialisation.hpp>
#include <iostream>
#include <sstream>
@@ -288,12 +289,13 @@ namespace libmaus2
uint64_t const numlines = (std::max(aa.size(),ba.size()) + linewidth-1) / linewidth;
uint64_t posa = rposa;
uint64_t posb = rposb;
+ uint64_t const numwidth = libmaus2::util::NumberSerialisation::formatNumber(std::max(rposa+an,rposb+bn),6).size();
for ( uint64_t i = 0; i < numlines; ++i )
{
uint64_t pl = i*linewidth;
- out << "A " << std::setw(6) << posa << std::setw(0) << " ";
+ out << "A " << std::setw(numwidth) << posa << std::setw(0) << " ";
if ( pl < aa.size() )
{
uint64_t const alen = std::min(linewidth,aa.size()-pl);
@@ -305,7 +307,7 @@ namespace libmaus2
}
out << std::endl;
- out << "B " << std::setw(6) << posb << std::setw(0) << " ";
+ out << "B " << std::setw(numwidth) << posb << std::setw(0) << " ";
if ( pl < ba.size() )
{
uint64_t const blen = std::min(linewidth,ba.size()-pl);
@@ -317,7 +319,7 @@ namespace libmaus2
}
out << std::endl;
- out << std::string(9,' ');
+ out << std::string(numwidth + 3,' ');
if ( pl < ca.size() )
{
uint64_t const clen = std::min(linewidth,ca.size()-pl);
@@ -427,6 +429,7 @@ namespace libmaus2
std::string const ca = cstr.str();
uint64_t const linewidth = rlinewidth-2;
uint64_t const numlines = (std::max(aa.size(),ba.size()) + linewidth-1) / linewidth;
+ uint64_t const numwidth = libmaus2::util::NumberSerialisation::formatNumber(std::max(rposa+an,rposb+bn),6).size();
uint64_t posa = rposa;
uint64_t posb = rposb;
@@ -435,7 +438,7 @@ namespace libmaus2
{
uint64_t pl = i*linewidth;
- out << paid << ' ' << std::setw(6) << posa << std::setw(0) << " ";
+ out << paid << ' ' << std::setw(numwidth) << posa << std::setw(0) << " ";
if ( pl < aa.size() )
{
uint64_t const alen = std::min(linewidth,aa.size()-pl);
@@ -447,7 +450,7 @@ namespace libmaus2
}
out << std::endl;
- out << pbid << ' ' << std::setw(6) << posb << std::setw(0) << " ";
+ out << pbid << ' ' << std::setw(numwidth) << posb << std::setw(0) << " ";
if ( pl < ba.size() )
{
uint64_t const blen = std::min(linewidth,ba.size()-pl);
@@ -462,7 +465,7 @@ namespace libmaus2
out
<< std::string(midlen,' ') // id
<< std::string(1,' ') // space
- << std::string(6,' ') // pos
+ << std::string(numwidth,' ') // pos
<< std::string(1,' ') // space
;
if ( pl < ca.size() )
=====================================
src/libmaus2/sorting/SortingBufferedOutputFile.hpp
=====================================
@@ -388,7 +388,7 @@ namespace libmaus2
typedef typename sorter_type::unique_ptr_type sorter_ptr_type;
libmaus2::autoarray::AutoArray < sorter_ptr_type > ASO;
- static std::vector < std::string > computeVfn(std::string const & s, uint64_t const n)
+ static std::vector < std::string > computeVfn(std::string const & s, uint64_t const n, bool const registertmp)
{
std::vector < std::string > Vfn(n);
for ( uint64_t i = 0; i < n; ++i )
@@ -396,6 +396,9 @@ namespace libmaus2
std::ostringstream ostr;
ostr << s << "_" << std::setw(6) << std::setfill('0') << i;
Vfn[i] = ostr.str();
+
+ if ( registertmp )
+ libmaus2::util::TempFileRemovalContainer::addTempFile(Vfn[i]);
}
return Vfn;
}
@@ -411,14 +414,24 @@ namespace libmaus2
}
}
- SerialisingSortingBufferedOutputFileArray(std::string const & rfilename, uint64_t const n, uint64_t const bufsize = 1024ull)
- : Vfn(computeVfn(rfilename,n)), Porder(new order_type), order(*Porder), filename(rfilename), ASO(n)
+ static uint64_t getDefaultBufSize()
+ {
+ return 1024ull;
+ }
+
+ static bool getDefaultRegisterTmp()
+ {
+ return false;
+ }
+
+ SerialisingSortingBufferedOutputFileArray(std::string const & rfilename, uint64_t const n, uint64_t const bufsize = getDefaultBufSize(), bool const registertmp = getDefaultRegisterTmp())
+ : Vfn(computeVfn(rfilename,n,registertmp)), Porder(new order_type), order(*Porder), filename(rfilename), ASO(n)
{
setupFileArray(bufsize);
}
- SerialisingSortingBufferedOutputFileArray(std::string const & rfilename, uint64_t const n, order_type & rorder, uint64_t const bufsize = 1024ull)
- : Vfn(computeVfn(rfilename,n)), Porder(), order(rorder), filename(rfilename), ASO(n)
+ SerialisingSortingBufferedOutputFileArray(std::string const & rfilename, uint64_t const n, order_type & rorder, uint64_t const bufsize = getDefaultBufSize(), bool const registertmp = getDefaultRegisterTmp())
+ : Vfn(computeVfn(rfilename,n,registertmp)), Porder(), order(rorder), filename(rfilename), ASO(n)
{
setupFileArray(bufsize);
}
=====================================
src/test/testbamgetrefreg.cpp
=====================================
@@ -46,7 +46,7 @@ int main(int argc, char * argv[])
// check the alignment
bool const algnok = algn.checkCigar(Vref.at(algn.getRefID()).begin());
assert ( algnok );
- std::string const cref = Vref[algn.getRefID()].substr(algn.getPos()-algn.getFrontDel(),algn.getReferenceLength());
+ std::string const cref = Vref[algn.getRefID()].substr(algn.getPos(),algn.getReferenceLength());
std::string const sref = algn.getReferenceRegionViaMd();
if ( sref == cref )
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/commit/61eda99ce62c3f1485b0bd444bd3d827b056f9ab
--
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/commit/61eda99ce62c3f1485b0bd444bd3d827b056f9ab
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