ChangeLog

+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

 @%:@! /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

 @%:@! /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

 @%:@! /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/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@mpi-cbg.de], [libmaus2], [https://github.com/gt1/libmaus2])
+m4trace:configure.ac:1: -1- AC_INIT([libmaus2], [2.0.663], [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 2.0.657.
+# 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\\"

configure.ac

-AC_INIT(libmaus2,2.0.657,[tischler@mpi-cbg.de],[libmaus2],[https://github.com/gt1/libmaus2])
-LIBRARY_VERSION=2:657:0
+AC_INIT(libmaus2,2.0.663,[tischler@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

debian/changelog

+libmaus2 (2.0.663-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * TODO: Added override to debian sharedlibs helper that should go in
+    a later upload
+
+ -- Steffen Moeller <moeller@debian.org>  Wed, 28 Aug 2019 15:05:00 +0200
+
 libmaus2 (2.0.657-1) unstable; urgency=medium
 
   * New upstream version

debian/rules

@@ -13,10 +13,13 @@ export LC_ALL=C.UTF-8
 
 override_dh_install:
 	dh_install
+	# following override suggestion from suggestion of Andreas to Michael
+	# to overcome d-shlibmove bug on Jan 4, 2019
 	d-shlibmove --commit \
 		    --multiarch \
 		    --devunversioned \
 		    --exclude-la \
+	            --override s/libdeflate0-dev/libdeflate-dev/ \
 		    --movedev debian/tmp/usr/include/* usr/include \
 		    --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
 		    debian/tmp/usr/lib/*/*.so

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

 /*
     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 )