ChangeLog

+libmaus2 (2.0.694-1) unstable; urgency=medium
+
+  * add missing include statements
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 22 Jan 2020 09:26:35 +0100
+
+libmaus2 (2.0.693-1) unstable; urgency=medium
+
+  * add CodonMapper class
+  * add missing include directive in acgtnMap.hpp
+  * make printTrace method in protein::Align output positions
+  * add missing include directive in StdTerminatableSynchronousHeap
+  * remove direct calls of lock method for StdMutex and StdSpinLock where possible (use scope locks instead)
+  * remove OMPLock class
+  * improve error handling in StdThread/SimpleThreadPoolThread
+  * avoid unlimited lock in StdMutex
+  * do not use unlimited wait in StdSemaphore
+  * store source header lines in different array of VCFParser
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 21 Jan 2020 16:06:50 +0100
+
+libmaus2 (2.0.692-1) unstable; urgency=medium
+
+  * be more verbose in contig name parse failure of VCFSorter
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 08 Jan 2020 14:50:19 +0100
+
+libmaus2 (2.0.691-1) unstable; urgency=medium
+
+  * allow line wrapped FastA/FastQ output of BAM records in BamAlignmentDecoderBase
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 07 Jan 2020 16:14:12 +0100
+
+libmaus2 (2.0.690-1) unstable; urgency=medium
+
+  * add kmerCallbackPosFR function in KmerBase
+  * rename timeout based trywait to trylock in StdMutex
+  * refactor StdMutex
+  * allow faster comparison in SerialisingBuffer
+  * add getProcessedFraction method in VCFParser
+  * put additional checks in GrowingFreeList
+  * Add contig list replacement machinery in VCFParser
+  * clean up include directives in Chromosome/ChromosomeVectorMerge
+  * Add constructHeader functions in BamMultiAlignmentDecoderFactory
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 07 Jan 2020 08:33:57 +0100
+
 libmaus2 (2.0.689-1) unstable; urgency=medium
 
   * add isCoding,getStrand and getCDS in GTFData

INSTALL

-Installation Instructions
-*************************
-
-Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
-Inc.
-
-   Copying and distribution of this file, with or without modification,
-are permitted in any medium without royalty provided the copyright
-notice and this notice are preserved.  This file is offered as-is,
-without warranty of any kind.
-
-Basic Installation
-==================
-
-   Briefly, the shell command `./configure && make && make install'
-should configure, build, and install this package.  The following
-more-detailed instructions are generic; see the `README' file for
-instructions specific to this package.  Some packages provide this
-`INSTALL' file but do not implement all of the features documented
-below.  The lack of an optional feature in a given package is not
-necessarily a bug.  More recommendations for GNU packages can be found
-in *note Makefile Conventions: (standards)Makefile Conventions.
-
-   The `configure' shell script attempts to guess correct values for
-various system-dependent variables used during compilation.  It uses
-those values to create a `Makefile' in each directory of the package.
-It may also create one or more `.h' files containing system-dependent
-definitions.  Finally, it creates a shell script `config.status' that
-you can run in the future to recreate the current configuration, and a
-file `config.log' containing compiler output (useful mainly for
-debugging `configure').
-
-   It can also use an optional file (typically called `config.cache'
-and enabled with `--cache-file=config.cache' or simply `-C') that saves
-the results of its tests to speed up reconfiguring.  Caching is
-disabled by default to prevent problems with accidental use of stale
-cache files.
-
-   If you need to do unusual things to compile the package, please try
-to figure out how `configure' could check whether to do them, and mail
-diffs or instructions to the address given in the `README' so they can
-be considered for the next release.  If you are using the cache, and at
-some point `config.cache' contains results you don't want to keep, you
-may remove or edit it.
-
-   The file `configure.ac' (or `configure.in') is used to create
-`configure' by a program called `autoconf'.  You need `configure.ac' if
-you want to change it or regenerate `configure' using a newer version
-of `autoconf'.
-
-   The simplest way to compile this package is:
-
-  1. `cd' to the directory containing the package's source code and type
-     `./configure' to configure the package for your system.
-
-     Running `configure' might take a while.  While running, it prints
-     some messages telling which features it is checking for.
-
-  2. Type `make' to compile the package.
-
-  3. Optionally, type `make check' to run any self-tests that come with
-     the package, generally using the just-built uninstalled binaries.
-
-  4. Type `make install' to install the programs and any data files and
-     documentation.  When installing into a prefix owned by root, it is
-     recommended that the package be configured and built as a regular
-     user, and only the `make install' phase executed with root
-     privileges.
-
-  5. Optionally, type `make installcheck' to repeat any self-tests, but
-     this time using the binaries in their final installed location.
-     This target does not install anything.  Running this target as a
-     regular user, particularly if the prior `make install' required
-     root privileges, verifies that the installation completed
-     correctly.
-
-  6. You can remove the program binaries and object files from the
-     source code directory by typing `make clean'.  To also remove the
-     files that `configure' created (so you can compile the package for
-     a different kind of computer), type `make distclean'.  There is
-     also a `make maintainer-clean' target, but that is intended mainly
-     for the package's developers.  If you use it, you may have to get
-     all sorts of other programs in order to regenerate files that came
-     with the distribution.
-
-  7. Often, you can also type `make uninstall' to remove the installed
-     files again.  In practice, not all packages have tested that
-     uninstallation works correctly, even though it is required by the
-     GNU Coding Standards.
-
-  8. Some packages, particularly those that use Automake, provide `make
-     distcheck', which can by used by developers to test that all other
-     targets like `make install' and `make uninstall' work correctly.
-     This target is generally not run by end users.
-
-Compilers and Options
-=====================
-
-   Some systems require unusual options for compilation or linking that
-the `configure' script does not know about.  Run `./configure --help'
-for details on some of the pertinent environment variables.
-
-   You can give `configure' initial values for configuration parameters
-by setting variables in the command line or in the environment.  Here
-is an example:
-
-     ./configure CC=c99 CFLAGS=-g LIBS=-lposix
-
-   *Note Defining Variables::, for more details.
-
-Compiling For Multiple Architectures
-====================================
-
-   You can compile the package for more than one kind of computer at the
-same time, by placing the object files for each architecture in their
-own directory.  To do this, you can use GNU `make'.  `cd' to the
-directory where you want the object files and executables to go and run
-the `configure' script.  `configure' automatically checks for the
-source code in the directory that `configure' is in and in `..'.  This
-is known as a "VPATH" build.
-
-   With a non-GNU `make', it is safer to compile the package for one
-architecture at a time in the source code directory.  After you have
-installed the package for one architecture, use `make distclean' before
-reconfiguring for another architecture.
-
-   On MacOS X 10.5 and later systems, you can create libraries and
-executables that work on multiple system types--known as "fat" or
-"universal" binaries--by specifying multiple `-arch' options to the
-compiler but only a single `-arch' option to the preprocessor.  Like
-this:
-
-     ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
-                 CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
-                 CPP="gcc -E" CXXCPP="g++ -E"
-
-   This is not guaranteed to produce working output in all cases, you
-may have to build one architecture at a time and combine the results
-using the `lipo' tool if you have problems.
-
-Installation Names
-==================
-
-   By default, `make install' installs the package's commands under
-`/usr/local/bin', include files under `/usr/local/include', etc.  You
-can specify an installation prefix other than `/usr/local' by giving
-`configure' the option `--prefix=PREFIX', where PREFIX must be an
-absolute file name.
-
-   You can specify separate installation prefixes for
-architecture-specific files and architecture-independent files.  If you
-pass the option `--exec-prefix=PREFIX' to `configure', the package uses
-PREFIX as the prefix for installing programs and libraries.
-Documentation and other data files still use the regular prefix.
-
-   In addition, if you use an unusual directory layout you can give
-options like `--bindir=DIR' to specify different values for particular
-kinds of files.  Run `configure --help' for a list of the directories
-you can set and what kinds of files go in them.  In general, the
-default for these options is expressed in terms of `${prefix}', so that
-specifying just `--prefix' will affect all of the other directory
-specifications that were not explicitly provided.
-
-   The most portable way to affect installation locations is to pass the
-correct locations to `configure'; however, many packages provide one or
-both of the following shortcuts of passing variable assignments to the
-`make install' command line to change installation locations without
-having to reconfigure or recompile.
-
-   The first method involves providing an override variable for each
-affected directory.  For example, `make install
-prefix=/alternate/directory' will choose an alternate location for all
-directory configuration variables that were expressed in terms of
-`${prefix}'.  Any directories that were specified during `configure',
-but not in terms of `${prefix}', must each be overridden at install
-time for the entire installation to be relocated.  The approach of
-makefile variable overrides for each directory variable is required by
-the GNU Coding Standards, and ideally causes no recompilation.
-However, some platforms have known limitations with the semantics of
-shared libraries that end up requiring recompilation when using this
-method, particularly noticeable in packages that use GNU Libtool.
-
-   The second method involves providing the `DESTDIR' variable.  For
-example, `make install DESTDIR=/alternate/directory' will prepend
-`/alternate/directory' before all installation names.  The approach of
-`DESTDIR' overrides is not required by the GNU Coding Standards, and
-does not work on platforms that have drive letters.  On the other hand,
-it does better at avoiding recompilation issues, and works well even
-when some directory options were not specified in terms of `${prefix}'
-at `configure' time.
-
-Optional Features
-=================
-
-   If the package supports it, you can cause programs to be installed
-with an extra prefix or suffix on their names by giving `configure' the
-option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
-
-   Some packages pay attention to `--enable-FEATURE' options to
-`configure', where FEATURE indicates an optional part of the package.
-They may also pay attention to `--with-PACKAGE' options, where PACKAGE
-is something like `gnu-as' or `x' (for the X Window System).  The
-`README' should mention any `--enable-' and `--with-' options that the
-package recognizes.
-
-   For packages that use the X Window System, `configure' can usually
-find the X include and library files automatically, but if it doesn't,
-you can use the `configure' options `--x-includes=DIR' and
-`--x-libraries=DIR' to specify their locations.
-
-   Some packages offer the ability to configure how verbose the
-execution of `make' will be.  For these packages, running `./configure
---enable-silent-rules' sets the default to minimal output, which can be
-overridden with `make V=1'; while running `./configure
---disable-silent-rules' sets the default to verbose, which can be
-overridden with `make V=0'.
-
-Particular systems
-==================
-
-   On HP-UX, the default C compiler is not ANSI C compatible.  If GNU
-CC is not installed, it is recommended to use the following options in
-order to use an ANSI C compiler:
-
-     ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
-
-and if that doesn't work, install pre-built binaries of GCC for HP-UX.
-
-   HP-UX `make' updates targets which have the same time stamps as
-their prerequisites, which makes it generally unusable when shipped
-generated files such as `configure' are involved.  Use GNU `make'
-instead.
-
-   On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
-parse its `<wchar.h>' header file.  The option `-nodtk' can be used as
-a workaround.  If GNU CC is not installed, it is therefore recommended
-to try
-
-     ./configure CC="cc"
-
-and if that doesn't work, try
-
-     ./configure CC="cc -nodtk"
-
-   On Solaris, don't put `/usr/ucb' early in your `PATH'.  This
-directory contains several dysfunctional programs; working variants of
-these programs are available in `/usr/bin'.  So, if you need `/usr/ucb'
-in your `PATH', put it _after_ `/usr/bin'.
-
-   On Haiku, software installed for all users goes in `/boot/common',
-not `/usr/local'.  It is recommended to use the following options:
-
-     ./configure --prefix=/boot/common
-
-Specifying the System Type
-==========================
-
-   There may be some features `configure' cannot figure out
-automatically, but needs to determine by the type of machine the package
-will run on.  Usually, assuming the package is built to be run on the
-_same_ architectures, `configure' can figure that out, but if it prints
-a message saying it cannot guess the machine type, give it the
-`--build=TYPE' option.  TYPE can either be a short name for the system
-type, such as `sun4', or a canonical name which has the form:
-
-     CPU-COMPANY-SYSTEM
-
-where SYSTEM can have one of these forms:
-
-     OS
-     KERNEL-OS
-
-   See the file `config.sub' for the possible values of each field.  If
-`config.sub' isn't included in this package, then this package doesn't
-need to know the machine type.
-
-   If you are _building_ compiler tools for cross-compiling, you should
-use the option `--target=TYPE' to select the type of system they will
-produce code for.
-
-   If you want to _use_ a cross compiler, that generates code for a
-platform different from the build platform, you should specify the
-"host" platform (i.e., that on which the generated programs will
-eventually be run) with `--host=TYPE'.
-
-Sharing Defaults
-================
-
-   If you want to set default values for `configure' scripts to share,
-you can create a site shell script called `config.site' that gives
-default values for variables like `CC', `cache_file', and `prefix'.
-`configure' looks for `PREFIX/share/config.site' if it exists, then
-`PREFIX/etc/config.site' if it exists.  Or, you can set the
-`CONFIG_SITE' environment variable to the location of the site script.
-A warning: not all `configure' scripts look for a site script.
-
-Defining Variables
-==================
-
-   Variables not defined in a site shell script can be set in the
-environment passed to `configure'.  However, some packages may run
-configure again during the build, and the customized values of these
-variables may be lost.  In order to avoid this problem, you should set
-them in the `configure' command line, using `VAR=value'.  For example:
-
-     ./configure CC=/usr/local2/bin/gcc
-
-causes the specified `gcc' to be used as the C compiler (unless it is
-overridden in the site shell script).
-
-Unfortunately, this technique does not work for `CONFIG_SHELL' due to
-an Autoconf limitation.  Until the limitation is lifted, you can use
-this workaround:
-
-     CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
-
-`configure' Invocation
-======================
-
-   `configure' recognizes the following options to control how it
-operates.
-
-`--help'
-`-h'
-     Print a summary of all of the options to `configure', and exit.
-
-`--help=short'
-`--help=recursive'
-     Print a summary of the options unique to this package's
-     `configure', and exit.  The `short' variant lists options used
-     only in the top level, while the `recursive' variant lists options
-     also present in any nested packages.
-
-`--version'
-`-V'
-     Print the version of Autoconf used to generate the `configure'
-     script, and exit.
-
-`--cache-file=FILE'
-     Enable the cache: use and save the results of the tests in FILE,
-     traditionally `config.cache'.  FILE defaults to `/dev/null' to
-     disable caching.
-
-`--config-cache'
-`-C'
-     Alias for `--cache-file=config.cache'.
-
-`--quiet'
-`--silent'
-`-q'
-     Do not print messages saying which checks are being made.  To
-     suppress all normal output, redirect it to `/dev/null' (any error
-     messages will still be shown).
-
-`--srcdir=DIR'
-     Look for the package's source code in directory DIR.  Usually
-     `configure' can determine that directory automatically.
-
-`--prefix=DIR'
-     Use DIR as the installation prefix.  *note Installation Names::
-     for more details, including other options available for fine-tuning
-     the installation locations.
-
-`--no-create'
-`-n'
-     Run the configure checks, but stop before creating any output
-     files.
-
-`configure' also accepts some other, not widely useful, options.  Run
-`configure --help' for more details.

compile

-#! /bin/sh
-# Wrapper for compilers which do not understand '-c -o'.
-
-scriptversion=2012-10-14.11; # UTC
-
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
-# Written by Tom Tromey <tromey@cygnus.com>.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# This file is maintained in Automake, please report
-# bugs to <bug-automake@gnu.org> or send patches to
-# <automake-patches@gnu.org>.
-
-nl='
-'
-
-# We need space, tab and new line, in precisely that order.  Quoting is
-# there to prevent tools from complaining about whitespace usage.
-IFS=" ""	$nl"
-
-file_conv=
-
-# func_file_conv build_file lazy
-# Convert a $build file to $host form and store it in $file
-# Currently only supports Windows hosts. If the determined conversion
-# type is listed in (the comma separated) LAZY, no conversion will
-# take place.
-func_file_conv ()
-{
-  file=$1
-  case $file in
-    / | /[!/]*) # absolute file, and not a UNC file
-      if test -z "$file_conv"; then
-	# lazily determine how to convert abs files
-	case `uname -s` in
-	  MINGW*)
-	    file_conv=mingw
-	    ;;
-	  CYGWIN*)
-	    file_conv=cygwin
-	    ;;
-	  *)
-	    file_conv=wine
-	    ;;
-	esac
-      fi
-      case $file_conv/,$2, in
-	*,$file_conv,*)
-	  ;;
-	mingw/*)
-	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
-	  ;;
-	cygwin/*)
-	  file=`cygpath -m "$file" || echo "$file"`
-	  ;;
-	wine/*)
-	  file=`winepath -w "$file" || echo "$file"`
-	  ;;
-      esac
-      ;;
-  esac
-}
-
-# func_cl_dashL linkdir
-# Make cl look for libraries in LINKDIR
-func_cl_dashL ()
-{
-  func_file_conv "$1"
-  if test -z "$lib_path"; then
-    lib_path=$file
-  else
-    lib_path="$lib_path;$file"
-  fi
-  linker_opts="$linker_opts -LIBPATH:$file"
-}
-
-# func_cl_dashl library
-# Do a library search-path lookup for cl
-func_cl_dashl ()
-{
-  lib=$1
-  found=no
-  save_IFS=$IFS
-  IFS=';'
-  for dir in $lib_path $LIB
-  do
-    IFS=$save_IFS
-    if $shared && test -f "$dir/$lib.dll.lib"; then
-      found=yes
-      lib=$dir/$lib.dll.lib
-      break
-    fi
-    if test -f "$dir/$lib.lib"; then
-      found=yes
-      lib=$dir/$lib.lib
-      break
-    fi
-    if test -f "$dir/lib$lib.a"; then
-      found=yes
-      lib=$dir/lib$lib.a
-      break
-    fi
-  done
-  IFS=$save_IFS
-
-  if test "$found" != yes; then
-    lib=$lib.lib
-  fi
-}
-
-# func_cl_wrapper cl arg...
-# Adjust compile command to suit cl
-func_cl_wrapper ()
-{
-  # Assume a capable shell
-  lib_path=
-  shared=:
-  linker_opts=
-  for arg
-  do
-    if test -n "$eat"; then
-      eat=
-    else
-      case $1 in
-	-o)
-	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
-	  eat=1
-	  case $2 in
-	    *.o | *.[oO][bB][jJ])
-	      func_file_conv "$2"
-	      set x "$@" -Fo"$file"
-	      shift
-	      ;;
-	    *)
-	      func_file_conv "$2"
-	      set x "$@" -Fe"$file"
-	      shift
-	      ;;
-	  esac
-	  ;;
-	-I)
-	  eat=1
-	  func_file_conv "$2" mingw
-	  set x "$@" -I"$file"
-	  shift
-	  ;;
-	-I*)
-	  func_file_conv "${1#-I}" mingw
-	  set x "$@" -I"$file"
-	  shift
-	  ;;
-	-l)
-	  eat=1
-	  func_cl_dashl "$2"
-	  set x "$@" "$lib"
-	  shift
-	  ;;
-	-l*)
-	  func_cl_dashl "${1#-l}"
-	  set x "$@" "$lib"
-	  shift
-	  ;;
-	-L)
-	  eat=1
-	  func_cl_dashL "$2"
-	  ;;
-	-L*)
-	  func_cl_dashL "${1#-L}"
-	  ;;
-	-static)
-	  shared=false
-	  ;;
-	-Wl,*)
-	  arg=${1#-Wl,}
-	  save_ifs="$IFS"; IFS=','
-	  for flag in $arg; do
-	    IFS="$save_ifs"
-	    linker_opts="$linker_opts $flag"
-	  done
-	  IFS="$save_ifs"
-	  ;;
-	-Xlinker)
-	  eat=1
-	  linker_opts="$linker_opts $2"
-	  ;;
-	-*)
-	  set x "$@" "$1"
-	  shift
-	  ;;
-	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
-	  func_file_conv "$1"
-	  set x "$@" -Tp"$file"
-	  shift
-	  ;;
-	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
-	  func_file_conv "$1" mingw
-	  set x "$@" "$file"
-	  shift
-	  ;;
-	*)
-	  set x "$@" "$1"
-	  shift
-	  ;;
-      esac
-    fi
-    shift
-  done
-  if test -n "$linker_opts"; then
-    linker_opts="-link$linker_opts"
-  fi
-  exec "$@" $linker_opts
-  exit 1
-}
-
-eat=
-
-case $1 in
-  '')
-     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
-     exit 1;
-     ;;
-  -h | --h*)
-    cat <<\EOF
-Usage: compile [--help] [--version] PROGRAM [ARGS]
-
-Wrapper for compilers which do not understand '-c -o'.
-Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
-arguments, and rename the output as expected.
-
-If you are trying to build a whole package this is not the
-right script to run: please start by reading the file 'INSTALL'.
-
-Report bugs to <bug-automake@gnu.org>.
-EOF
-    exit $?
-    ;;
-  -v | --v*)
-    echo "compile $scriptversion"
-    exit $?
-    ;;
-  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
-    func_cl_wrapper "$@"      # Doesn't return...
-    ;;
-esac
-
-ofile=
-cfile=
-
-for arg
-do
-  if test -n "$eat"; then
-    eat=
-  else
-    case $1 in
-      -o)
-	# configure might choose to run compile as 'compile cc -o foo foo.c'.
-	# So we strip '-o arg' only if arg is an object.
-	eat=1
-	case $2 in
-	  *.o | *.obj)
-	    ofile=$2
-	    ;;
-	  *)
-	    set x "$@" -o "$2"
-	    shift
-	    ;;
-	esac
-	;;
-      *.c)
-	cfile=$1
-	set x "$@" "$1"
-	shift
-	;;
-      *)
-	set x "$@" "$1"
-	shift
-	;;
-    esac
-  fi
-  shift
-done
-
-if test -z "$ofile" || test -z "$cfile"; then
-  # If no '-o' option was seen then we might have been invoked from a
-  # pattern rule where we don't need one.  That is ok -- this is a
-  # normal compilation that the losing compiler can handle.  If no
-  # '.c' file was seen then we are probably linking.  That is also
-  # ok.
-  exec "$@"
-fi
-
-# Name of file we expect compiler to create.
-cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
-
-# Create the lock directory.
-# Note: use '[/\\:.-]' here to ensure that we don't use the same name
-# that we are using for the .o file.  Also, base the name on the expected
-# object file name, since that is what matters with a parallel build.
-lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
-while true; do
-  if mkdir "$lockdir" >/dev/null 2>&1; then
-    break
-  fi
-  sleep 1
-done
-# FIXME: race condition here if user kills between mkdir and trap.
-trap "rmdir '$lockdir'; exit 1" 1 2 15
-
-# Run the compile.
-"$@"
-ret=$?
-
-if test -f "$cofile"; then
-  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
-elif test -f "${cofile}bj"; then
-  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
-fi
-
-rmdir "$lockdir"
-exit $ret
-
-# Local Variables:
-# mode: shell-script
-# sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:

configure.ac

-AC_INIT(libmaus2,2.0.689,[tischler@mpi-cbg.de],[libmaus2],[https://github.com/gt1/libmaus2])
-LIBRARY_VERSION=2:689:0
+AC_INIT(libmaus2,2.0.694,[tischler@mpi-cbg.de],[libmaus2],[https://github.com/gt1/libmaus2])
+LIBRARY_VERSION=2:694:0
 AC_MSG_NOTICE([Configuring for source in directory ${srcdir}])
 AC_CANONICAL_SYSTEM
 AC_CANONICAL_HOST

debian/changelog

+libmaus2 (2.0.694+ds-1) unstable; urgency=medium
+
+  * New upstream version
+  * Added myself as uploader.
+  * Standards-Version: 4.5.0
+  * Set upstream metadata fields: Bug-Database, Repository, Repository-
+    Browse.
+  * Removing autogenerated files that upstream intentionally adds
+    to the release.
+
+ -- Steffen Moeller <moeller@debian.org>  Thu, 23 Jan 2020 10:20:02 +0100
+
 libmaus2 (2.0.689-1) unstable; urgency=medium
 
   * New upstream version

debian/control

 Source: libmaus2
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille@debian.org>
+Uploaders: Andreas Tille <tille@debian.org>,
+           Steffen Moeller <moeller@debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
                d-shlibs,
                pkg-config,
                zlib1g-dev
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/libmaus2
 Vcs-Git: https://salsa.debian.org/med-team/libmaus2.git
 Homepage: https://gitlab.com/german.tischler/libmaus2

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: libmaus2
 Source: https://gitlab.com/german.tischler/libmaus2/tags
+Files-Excluded:
+ INSTALL
+ Makefile.in
+ aclocal.m4
+ compile
+ config.guess
+ config.sub
+ configure
+ depcomp
+ install-sh
+ ltmain.sh
+ m4/libtool.m4
+ missing
+ src/Makefile.in
+ test/Makefile.in
+ autom4te.cache/*
 
 Files: *
 Copyright: 2010-2016 German Tischler

debian/upstream/metadata

@@ -7,3 +7,6 @@ Registry:
   Entry: libmaus
   Comment: No refereral to a version 2
 Bug-Submit: tischler@mpi-cbg.de
+Bug-Database: https://gitlab.com/german.tischler/libmaus2/issues
+Repository: https://gitlab.com/german.tischler/libmaus2.git
+Repository-Browse: https://gitlab.com/german.tischler/libmaus2