.gitignore

+# Ignore locally built doxygen documentation
+documentation/doxygen/doxygen_sqlite3.db
+documentation/doxygen/html/
+documentation/doxygen/latex/
+
+# Ignore .DS_Store that is known to clutter repositories on MacOS
+.DS_Store
\ No newline at end of file

.gitlab-ci.yml

+image: alpine
+
+before_script:
+  - apk update
+  - apk add doxygen
+  ## Uncomment the following line if you use graphviz dot graphs
+  - apk add ttf-freefont graphviz
+
+test:
+  script:
+  ## execute doxygen
+  - doxygen documentation/doxygen/config.doxyfile
+  except:
+  - master
+  
+#pages:
+#  script:
+#  ## execute doxygen
+#  - doxygen documentation/doxygen/config.doxyfile
+#  ## Move documentation/doxygen/html/ to public
+#  - mv documentation/doxygen/html/ public/
+#  artifacts:
+#    paths: 
+#    - public
+#  only:
+#  ## Branch
+#  - master				

CHANGELOG.md

-HiLive - Live Mapping of Illumina reads
-=======================================
-
 Changelog
------------
+=========
+
+v2.0
+-----
+
+Version 2.0 comes with a completely new index and algorithm.  
+This comes with major changes in parameter settings.  
+Please note, that commands and index files of previous versions cannot be used with HiLive v2.0.  
+The old HiLive version using the k-mer seed-and-extend approach is still available in a separated repository.  
+Please visit https://gitlab.com/rki_bioinformatics/HiLive for access to both versions.
+
+General functionality:
+ * New algorithm based on the FM-index
+ * Exact mapping results after a potential front softclip
+ * Support of alternative scoring models other than edit distance
+
+Parameters:
+ * Revised parameter nomenclature
+ * Multitoken parameters must now be comma-separated
+ * Changed config file format to .ini
+ * Additional parameters to facilitate parameter input (e.g., --max-tile for easier tile declaration)
+ * Different alignment modes for automated selection of algorithmic parameters
+
+Output:
+ * Corrected SAM flags for paired-end reads.
 
 v1.1
 -----

CMakeLists.txt

 ##############
 ### Header ###
+##############
 
-cmake_minimum_required (VERSION 2.8)
-project (HiLive)
-
-# Set the version number 
-add_definitions(-DHiLive_VERSION_MAJOR=1)
-add_definitions(-DHiLive_VERSION_MINOR=1)
+cmake_minimum_required( VERSION 3.10 FATAL_ERROR )
+project( HiLive VERSION 2.0 LANGUAGES CXX )
+
+###################
+### Build Setup ###
+###################
+
+# Set CXX Standard
+set( CMAKE_CXX_STANDARD 14 )
+set( CMAKE_CXX_SANDARD_REQUIRED ON )
+set( CMAKE_CXX_EXTENSIONS OFF )
+
+# Set runtime output directory
+set( CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR} )
+
+# Error on unsupported compiler
+if( NOT CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU" )
+    message( FATAL_ERROR
+        "Compiler id '${CMAKE_CXX_COMPILER_ID}' is not supported, please \
+        check the documentation." )
+endif()
+
+# Compiling options
+option( VERBOSE_CONFIG "Verbose mode for quick build setup debugging." OFF )
+option( CONDA "Flag for compilation in conda env." OFF )
+option( LZ4_PATH "Path to manually installed LZ4 library." "")
+option( SEQAN_PATH "Path to manually installed SeqAn library." "")
+option( BOOST_PATH "Path to manually installed Boost library." "")
+option( STRICT_WARN "Flag for strict warnings." OFF )
+
+# Set HiLive2 compile-time variables 
+add_definitions(-DHiLive_VERSION_MAJOR=2)
+add_definitions(-DHiLive_VERSION_MINOR=0)
+
+###################
+### Build types ###
+###################
+
+# Release flags
+set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" )
+
+# Warning flags
+if ( STRICT_WARN )
+	add_compile_options( -Wall -Wextra -Wshadow -Wuninitialized -Wnon-virtual-dtor
+		-Wold-style-cast -Wcast-align -Wunused -Woverloaded-virtual -Wpedantic
+		-Wconversion -Wsign-conversion -Wdouble-promotion
+		-Wformat=2 -Wstrict-aliasing -Wno-long-long -Wno-variadic-macros )
+endif()
+
+# SeqAn specific flags
+if ( NOT CONDA )
+	add_compile_options( -static -march=native )
+endif()
 
 # Set flags for compilation
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -g -pthread -W -Wall -std=gnu++14 -O0")
+# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -g -pthread -W -Wall -std=gnu++14 -O0")
 
 # add the binary tree to the search path for include files
 include_directories("${PROJECT_BINARY_DIR}")
 
 
-#############################
-### setup Boost libraries ###
+############################################
+### Dependencies and 3rd party libraries ###
+############################################
 
+# BOOST
+if ( BOOST_PATH )
+	set( Boost_NO_BOOST_CMAKE TRUE )
+	set( Boost_NO_SYSTEM_PATHS TRUE )
+	set( BOOST_ROOT "${BOOST_PATH}" )
+	set( Boost_LIBRARY_DIRS "${BOOST_PATH}/lib" ) 
+endif()
 set(Boost_USE_STATIC_LIBS ON) 
 set(Boost_USE_MULTITHREADED ON)  
 set(Boost_USE_STATIC_RUNTIME ON) 
-find_package( Boost COMPONENTS system filesystem program_options REQUIRED )
+find_package( Boost COMPONENTS system filesystem program_options iostreams REQUIRED )
 include_directories( ${Boost_INCLUDE_DIR} )
 
-
-############################
-### setup Zlib and lz4 libraries ###
-
+# ZLIB
 find_package( ZLIB REQUIRED )
-#set (LZ4_PATH /usr/local/lib) 		# possibly adjust this to [pathToLz4]/lib if using downloaded lz4 source code
-include_directories(${LZ4_PATH})
-link_directories(${LZ4_PATH})
-set(CompressionLibs "${ZLIB_LIBRARIES};lz4")
 
+# LZ4
+if ( LZ4_PATH )
+	set( LZ4_LIB "${LZ4_PATH}/lib" )
+endif()
 
-#############################
-### setup seqan libraries ### needs to be done AFTER searching for Zlib
+include_directories(${LZ4_LIB})
+link_directories(${LZ4_LIB})
+set(CompressionLibs "${ZLIB_LIBRARIES};lz4")
 
-set (CMAKE_MODULE_PATH "/usr/local/lib/seqan/util/cmake") # adjust this to [pathToSeqanCode]/util/cmake
-set (SEQAN_INCLUDE_PATH "/usr/local/lib/seqan/include/") # adjust this to [pathToSeqanCode]/include
+# SEQAN
+if ( SEQAN_PATH )
+	set (CMAKE_MODULE_PATH "${SEQAN_PATH}/util/cmake") 
+	set (SEQAN_INCLUDE_PATH "${SEQAN_PATH}/include/") 
+endif()
 
-# Configure SeqAn, enabling features for libbz2 and zlib.
-#set (SEQAN_FIND_DEPENDENCIES ZLIB BZip2) # original version from seqan tutorial
-set (SEQAN_FIND_DEPENDENCIES BZip2)
 find_package (SeqAn REQUIRED)
 
 # Add include directories, defines, and flags for SeqAn (and its dependencies).
+add_library( SeqAn INTERFACE )
 include_directories (${SEQAN_INCLUDE_DIRS})
-add_definitions (${SEQAN_DEFINITIONS})
+add_compile_options( ${SEQAN_DEFINITIONS} )
 set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")
 
 
 ##############################
 ### setup HiLive libraries ###
+##############################
+
 include_directories("${PROJECT_SOURCE_DIR}/lib")
+
 # make a list of HiLive libraries
-set (LIB_NAMES tools_static tools alnread alnstream illumina_parsers kindex parallel argument_parser)
+set (LIB_NAMES tools_static tools alnread alnstream alnout illumina_parsers kindex parallel argument_parser)
 set(LIB_LIST "")
 foreach (x ${LIB_NAMES})
 	list(APPEND LIB_LIST "lib/${x}.cpp")
 endforeach()
 add_library(HiLiveLibs ${LIB_LIST})
 
-
 #############################
 ### Build the executables ###
 
@@ -76,11 +133,3 @@ target_link_libraries(hilive-build HiLiveLibs ${CompressionLibs} ${Boost_LIBRARI
 add_executable(hilive-out tools/hilive_out.cpp )
 target_link_libraries(hilive-out HiLiveLibs ${CompressionLibs} ${Boost_LIBRARIES} ${SEQAN_LIBRARIES})
 
-
-#####################
-### for debugging ###
-
-#get_cmake_property(_variableNames VARIABLES)
-#foreach (_variableName ${_variableNames})
-	#message(STATUS "${_variableName}=${${_variableName}}")
-#endforeach()

CONTRIBUTORS → CONTRIBUTORS.md

-Bernhard Y. Renard <renardb (at) rki.de>
- * Project head
+Contributors
+============
 
-Martin S. Lindner <martin (at) mail-linder.de>
- * Project founder, implemented versions 0.1 and 0.2
+Active contributors
+-----
 
-Jakob M. Schulze <jakobschulze (at) arcor.de>
- * development v0.2 -> v0.3
- * development support v0.3 -> v1.0
+Bernhard Y. Renard <renardb (at) rki.de>
+ * Project head
 
 Tobias P. Loka <lokat (at) rki.de>
- * development v0.3 -> v1.0
- * development v1.0 -> v1.1
+ * Development HiLive v2.0 (HiLive2)
+ * Development HiLive v1.1
+ * Development HiLive v1.0
 
 Simon H. Tausch <tauschs (at) rki.de>
  * continuous development support
 
+
+Former contributors
+-----
+
+Martin S. Lindner <martin (at) mail-linder.de>
+ * Development HiLive v0.2
+ * Development HiLive v0.1
+ * Project founder
+
+Jakob M. Schulze <jakobschulze (at) arcor.de>
+ * Development support v1.0
+ * Development v0.3
+ 
  Kristina Kirsten
- * development support v0.3 -> v1.0 (real-time SAM/BAM output)
\ No newline at end of file
+ * Development support v1.0

LICENSE → LICENSE.md

-Copyright (c) 2015-2017, Martin S. Lindner and the HiLive contributors. See CONTRIBUTORS for more info.
+License
+=======
+
+Copyright (c) 2015-2018, Martin S. Lindner and the HiLive contributors. See CONTRIBUTORS.md for more info.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

README.md

-HiLive - Live Mapping of Illumina reads
-=======================================
+<!-- {#mainpage} -->
+
+HiLive2 - Live Mapping of Illumina reads
+========================================
+
+- [Description](#description)
+- [Website](#website)
+- [Installation](#installation)
+- [Usage](#usage)
+- [License](#license)
+- [Contact](#contact)
 
 Description
 -----------
 
-HiLive is a read mapping tool that maps Illumina HiSeq (or comparable) 
+HiLive2 is a read mapping tool that maps Illumina HiSeq (or comparable) 
 reads right in the moment when they are produced. This means, read mapping 
-is finished as soon as the sequencer is finished.
+is finished as soon as the sequencer is finished. Alignment output can also 
+be written for intermediate cycles providing insights into the data already 
+during sequencing. HiLive2 supports paired-end reads and live demultiplexing, 
+creating one output alignment file for each barcode and cycle.
 
 
 Website
 -------
 
-The HiLive project website is https://gitlab.com/SimonHTausch/HiLive
+The general HiLive project website is 
+https://gitlab.com/rki_bioinformatics/HiLive.  
+Here, you find information and links to HiLive and HiLive2.  
+
+The direct link to HiLive2 is https://gitlab.com/LokaT/HiLive2.  
+There you can find the latest version of HiLive2, source code, documentation and
+example data.  
 
-There you can find the latest version of HiLive, source code, documentation,
-and examples.
+Please report bugs and problems by 
+[opening an issue](https://gitlab.com/LokaT/HiLive2/issues) or mail us to 
+hilive.team (at) gmail.com.
 
 
 Installation
 ------------
 
-If you are using a Debian based system you can directly install the Debian 
-package from the official [Debian repository](https://packages.debian.org/sid/hilive "HiLive Debian package")
+HiLive2 can currently only be installed from source.  
 
-If this does not work for you, you can still compile HiLive from source.
+The following dependencies are required:
 
-Make sure that the following dependencies are installed:
-
- * cmake (>= 2.8)
- * boost (system, filesystem, program\_options)
+ * cmake (>= 3.10)
+ * boost (system, filesystem, program\_options, iostreams)
  * zlib
  * lz4
-
-If using a local version of lz4 then adjust path in CMakeLists.txt line 32.
+ * [SeqAn](http://packages.seqan.de/) (version 2.3.2)
 
 ---
 
-You also need to download download seqan.
-Cloning the repository makes it possible to switch between different versions:
-
-    git clone https://github.com/seqan/seqan.git
-
-HiLive 1.0 was tested with SeqAn version 2.3.2.
-
----
+Check out the HiLive2 source code from the project website and `make` the 
+project.  
+We recommend to have separated `source` and `build` directories:
 
-Check out the HiLive source code from the project website and adjust the paths of the
-seqan module in the file CMakeLists.txt in the hilive folder (line 41 and 42).
-Then, compile HiLive with:
-
-    cd [hilive-code]
+```
+mkdir HiLive2 && cd HiLive2
+git clone https://gitlab.com/LokaT/HiLive2 source
 mkdir build && cd build
-    cmake ..
+cmake ../source -DSEQAN_PATH="PATH/TO/UNPACKED/SEQAN/"
 make
+```
+
+If using local versions of boost or lz4, please specify the path with the `cmake` command using `-DLZ4_PATH="/PATH/TO/LZ4"` and `-DBOOST_PATH="/PATH/TO/BOOST"`, respectively.  
+
 
 Usage
 -----
 
-HiLive has three components:
+HiLive2 has three components:
 
- * ``hilive-build``  builds the k-mer index of the reference genome
+ * ``hilive-build``  builds the index of a reference genome
  * ``hilive``        the read mapper itself
- * ``hilive-out``    executable to produce output files
-
----
+ * ``hilive-out``    write output files of existing HiLive data
 
 #### Using hilive-build:
 
-Building a k-mer index from FASTA file input.fa to output file input.fa.kix with k-mer weight 15:
-
-    hilive-build input.fa 15
-
-Building an index from a large reference genome. Here is makes sense to use trimming,
-i.e. removing k-mers from the index that occurr more than 1000 times (for example) in
-the index. The index is written into the file trimmed.kix
-
-    hilive-build -t 1000 -o trimmed.kix input.fa 15
+Building a HiLive2 index from FASTA file input.fa:
 
-For gapped k-mers, use the -p parameter to specify the gap positions.
-For example, for a gap pattern of 1101110011, type:
+```
+hilive-build --input input.fa --out-prefix /path/to/index/directory/prefix
+```
 
-    hilive-build -p 3 7 8 input.fa 7
-    
-With the current index structure, we strongly recommend to use a maximum k-mer weight of 15 because of huge disk space and memory requirements for large 
-k-mers.
-
----
+The command will produce several files with the declared prefix.  
 
 #### Using hilive:
 
-To map reads in a 100bp run using default settings:
+To map reads in a 100bp run (without barcodes) using default settings:
 
-    hilive /path/to/BaseCalls /path/to/index.kix 100 /path/to/outputFolder
+    hilive --bcl-dir /path/to/BaseCalls --index /path/to/prefix --reads 100R
 
 For an overview of additional parameters, type 
 	
 	hilive --help
 
-To prevent errors during argument parsing we recommend to set optional parameters AFTER the positional options:
-
-	hilive BC_DIR INDEX CYCLES OUTDIR [options]
-	
-However, if unexpected parsing errors occur, please try to specify all parameters with the "--"-syntax (e.g. --BCDIR /path/to/BaseCalls) instead of using positional arguments. This is also necessary when loading (some of the) positional arguments from a settings file instead of using the command line.
-
----
-
 #### Using hilive-out:
 
-To create a SAM or BAM alignment output from existing temporary files in HiLive, type:
+hilive-out required a config file as input.  
+This should be the config file that is automatically written in the temporary 
+directory of the original HiLive2 run.  
+To write output from existing temporary files in HiLive, type:
 
-	hilive-out --settings /path/to/temp/dir/hilive_settings.xml
+```
+hilive-out --config /path/to/temp/hilive_config.ini
+```
 
-This will output the alignment results of the last cycle based on the settings that were specified for the related HiLive run.
-To produce output files for other cycles, e.g. 50, 70, 90, type:
+This command will report the alignment results of the last cycle based on the 
+settings that were specified for the related HiLive2 run. To produce output 
+files for other cycles, e.g. 50, 70, 90, type:
 
-	hilive-out --settings /path/to/temp/dir/hilive_settings.xml --output-cycles 50 70 90
-	
-Please note, that the temporary files for the respective cycles must be present in the temp folder.
-This is only the case if the --keep-files parameter and/or the --output-cycles parameter for the respective cycles was activated in the HiLive run.
-
-
-#### Demultiplexing:
-
-To map reads from multiplexed sequencing runs, you can provide HiLive with the barcode sequences from your Sample Sheet.
-In default cases, barcode sequences are read after the (first) read, such that demultiplexing is carried out after the mapping is completed. 
-If you use double indexing, please concatenate both indices in the correct order and provide them as one sequence. Please take care that the number of cycles is exactly the read length from your Sample Sheet plus that of your complete barcode sequence. All entered indices must be of the same length. To provide multiple indices, enter the -XXX argument for every barcode or barcode combination, e.g.:
-
-	hilive /path/to/BaseCalls /path/to/index.kix 107 /path/to/outputFolder -b barcode1 -b barcode2 ...
-
-One output file will be produced for each barcode. To get alignments with undetermined barcodes, activate the --keep-all-barcodes parameter.
-Dual barcodes must be delimited with "-" (e.g., -b ATCGTGAT-TAGTTAGC for a 2x8bp barcode).
-
----
+```
+hilive-out --config /path/to/temp/hilive_config.ini --out-cycles 50,70,90
+```
 
-Please consult the project website for more details on the parameters!
+#### Tutorial
+We provide more extensive explanations and examples in the [Tutorial](https://gitlab.com/lokat/hilive2/tutorial).
 
 
 License
@@ -149,7 +131,8 @@ Contact
 Please consult the HiLive project website for questions!
 
 If this does not help, please feel free to consult:
- * Technical support <hilive.team (at) gmail.com> (technical contact)
- * Bernhard Y. Renard <renardb (at) rki.de> (project head)
+ * Technical support: hilive.team (at) gmail.com (technical contact)
+ * Bernhard Y. Renard: renardb (at) rki.de (project head)
 
-also see CONTRIBUTORS for a complete list of contributors and their contact information
+also see CONTRIBUTORS for a complete list of contributors and their contact 
+information.

debian/changelog

+hilive (2.0a-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * New URL on Github
+  * Fix watch file
+  * Standards-Version: 4.4.1
+  * Build-Depends: libboost-iostreams-dev
+
+ -- Andreas Tille <tille@debian.org>  Mon, 07 Oct 2019 11:02:50 +0200
+
 hilive (1.1-3) unstable; urgency=medium
 
   * Fix watch file

debian/control

@@ -7,16 +7,17 @@ Build-Depends: debhelper-compat (= 12),
                cmake,
                libboost-system-dev,
                libboost-filesystem-dev,
+               libboost-iostreams-dev,
                libboost-program-options-dev,
                libhts-dev,
                libseqan2-dev,
                zlib1g-dev,
                liblz4-dev,
                chrpath
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/hilive
 Vcs-Git: https://salsa.debian.org/med-team/hilive.git
-Homepage: https://gitlab.com/SimonHTausch/HiLive
+Homepage: https://gitlab.com/rki_bioinformatics/HiLive2
 
 Package: hilive
 Architecture: any

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: HiLive
-Source: https://gitlab.com/SimonHTausch/HiLive
+Upstream-Name: HiLive2
+Source: https://gitlab.com/rki_bioinformatics/HiLive2
 
 Files: *
 Copyright: 2015 Martin S. Lindner <marzin@mail-lindner.de>
+           2015-2018 Simon Tausch <TauschS@rki.de>
+           2018-2019 Tobias Loka <LokaT@rki.de>
 License: BSD-3-clause
 
 Files: debian/*
-Copyright: 2016 Andreas Tille <tille@debian.org>
+Copyright: 2016-2019 Andreas Tille <tille@debian.org>
 License: BSD-3-clause
 
 License: BSD-3-clause

debian/patches/do_not_set_rpath.patch

@@ -7,11 +7,10 @@ Description: Do not set rpath
 
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -62,7 +62,7 @@ foreach (x ${LIB_NAMES})
+@@ -120,6 +120,7 @@ foreach (x ${LIB_NAMES})
  	list(APPEND LIB_LIST "lib/${x}.cpp")
  endforeach()
  add_library(HiLiveLibs ${LIB_LIST})
--
 +set_target_properties(HiLiveLibs PROPERTIES SKIP_BUILD_RPATH TRUE)
  
  #############################

debian/patches/series

 do_not_set_rpath.patch
 use_FindSeQan.patch
+use_dynamic_linking.patch

debian/patches/use_FindSeQan.patch

@@ -3,15 +3,14 @@ Author: Gert Wollny <gw.fossdev@gmail.com>
 
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -38,8 +38,9 @@ set(CompressionLibs "${ZLIB_LIBRARIES};l
- #############################
- ### setup seqan libraries ### needs to be done AFTER searching for Zlib
+@@ -94,8 +94,8 @@ set(CompressionLibs "${ZLIB_LIBRARIES};l
  
--set (CMAKE_MODULE_PATH "/usr/local/lib/seqan/util/cmake") # adjust this to [pathToSeqanCode]/util/cmake
--set (SEQAN_INCLUDE_PATH "/usr/local/lib/seqan/include/") # adjust this to [pathToSeqanCode]/include
-+set (CMAKE_MODULE_PATH "/usr/share/cmake/") # adjust this to [pathToSeqanCode]/util/cmake
-+set (SEQAN_INCLUDE_PATH "/usr/lib/seqan/include/") # adjust this to [pathToSeqanCode]/include
-+set (SeqAn_DIR "/usr/share/cmake") # hint from Sascha Steinbiss <satta@debian.org>
+ # SEQAN
+ if ( SEQAN_PATH )
+-	set (CMAKE_MODULE_PATH "${SEQAN_PATH}/util/cmake") 
+-	set (SEQAN_INCLUDE_PATH "${SEQAN_PATH}/include/") 
++	set (CMAKE_MODULE_PATH "/usr/share/cmake/seqan/seqan-config.cmake") 
++	set (SEQAN_INCLUDE_PATH "/usr/include/seqan") 
+ endif()
  
- # Configure SeqAn, enabling features for libbz2 and zlib.
- #set (SEQAN_FIND_DEPENDENCIES ZLIB BZip2) # original version from seqan tutorial
+ find_package (SeqAn REQUIRED)

debian/patches/use_dynamic_linking.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 07 Oct 2019 11:02:50 +0200
+Description: Do not link statically; -pthread option (otherwise its -lpthread which does not work)
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -53,11 +53,12 @@ endif()
+ 
+ # SeqAn specific flags
+ if ( NOT CONDA )
+-	add_compile_options( -static -march=native )
++	add_compile_options( -march=native )
+ endif()
+ 
+ # Set flags for compilation
+ # set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -g -pthread -W -Wall -std=gnu++14 -O0")
++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
+ 
+ # add the binary tree to the search path for include files
+ include_directories("${PROJECT_BINARY_DIR}")
+@@ -74,9 +75,9 @@ if ( BOOST_PATH )
+ 	set( BOOST_ROOT "${BOOST_PATH}" )
+ 	set( Boost_LIBRARY_DIRS "${BOOST_PATH}/lib" ) 
+ endif()
+-set(Boost_USE_STATIC_LIBS ON) 
++set(Boost_USE_STATIC_LIBS OFF) 
+ set(Boost_USE_MULTITHREADED ON)  
+-set(Boost_USE_STATIC_RUNTIME ON) 
++set(Boost_USE_STATIC_RUNTIME OFF) 
+ find_package( Boost COMPONENTS system filesystem program_options iostreams REQUIRED )
+ include_directories( ${Boost_INCLUDE_DIR} )
+ 

debian/rules

@@ -4,9 +4,15 @@
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
 
+DEB_CMAKE_EXTRA_FLAGS += \
+        -DSEQAN_PATH=/usr/lib/seqan/
+
 %:
 	dh $@
 
+override_dh_auto_configure:
+	dh_auto_configure -- $(DEB_CMAKE_EXTRA_FLAGS)
+
 override_dh_install:
 	chrpath --delete obj-$(DEB_BUILD_GNU_TYPE)/hilive*
 	dh_install

debian/watch

 version=4
 
-opts="filenamemangle=s/@ANY_VERSION@\/.*\.tar\.gz/HiLive-$1\.tar\.gz/g,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
-  https://gitlab.com/SimonHTausch/HiLive/tags?sort=updated_desc .*/archive/v@ANY_VERSION@/HiLive-v.*\.tar\.gz
+https://gitlab.com/rki_bioinformatics/HiLive2/tags?sort=updated_desc .*/archive/v@ANY_VERSION@/HiLive2-v.*\.tar\.gz

documentation/doxygen/DoxygenLayout.xml

+<doxygenlayout version="1.0">
+  <!-- Generated by doxygen 1.8.11 -->
+  <!-- Navigation index tabs for HTML output -->
+  <navindex>
+    <tab type="mainpage" visible="yes" title="Quickstart Guide"/>
+    <tab type="pages" visible="yes" title="" intro=""/>
+    <tab type="modules" visible="yes" title="" intro=""/>
+    <tab type="namespaces" visible="yes" title="">
+      <tab type="namespacelist" visible="yes" title="" intro=""/>
+      <tab type="namespacemembers" visible="yes" title="" intro=""/>
+    </tab>
+    <tab type="classes" visible="yes" title="">
+      <tab type="classlist" visible="yes" title="" intro=""/>
+      <tab type="classindex" visible="$ALPHABETICAL_INDEX" title=""/> 
+      <tab type="hierarchy" visible="yes" title="" intro=""/>
+      <tab type="classmembers" visible="yes" title="" intro=""/>
+    </tab>
+    <tab type="files" visible="yes" title="">
+      <tab type="filelist" visible="yes" title="" intro=""/>
+      <tab type="globals" visible="yes" title="" intro=""/>
+    </tab><tab type="examples" visible="yes" title="" intro="" />
+    
+    <tab title="MF1: Bioinformatics" type="usergroup" visible="yes">
+    	<tab type="user" title="Official Website"
+    		url="https://www.rki.de/EN/Content/Institute/DepartmentsUnits/MF/MF1/mf1_node.html"
+    		visible="yes">
+    	</tab>
+    	<tab title="GitLab Software Repository" url="https://gitlab.com/rki_bioinformatics" visible="yes" type="user"></tab>
+    </tab>
+
+  </navindex>
+
+  <!-- Layout definition for a class page -->
+  <class>
+    <briefdescription visible="yes"/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <inheritancegraph visible="$CLASS_GRAPH"/>
+    <collaborationgraph visible="$COLLABORATION_GRAPH"/>
+    <memberdecl>
+      <nestedclasses visible="yes" title=""/>
+      <publictypes title=""/>
+      <services title=""/>
+      <interfaces title=""/>
+      <publicslots title=""/>
+      <signals title=""/>
+      <publicmethods title=""/>
+      <publicstaticmethods title=""/>
+      <publicattributes title=""/>
+      <publicstaticattributes title=""/>
+      <protectedtypes title=""/>
+      <protectedslots title=""/>
+      <protectedmethods title=""/>
+      <protectedstaticmethods title=""/>
+      <protectedattributes title=""/>
+      <protectedstaticattributes title=""/>
+      <packagetypes title=""/>
+      <packagemethods title=""/>
+      <packagestaticmethods title=""/>
+      <packageattributes title=""/>
+      <packagestaticattributes title=""/>
+      <properties title=""/>
+      <events title=""/>
+      <privatetypes title=""/>
+      <privateslots title=""/>
+      <privatemethods title=""/>
+      <privatestaticmethods title=""/>
+      <privateattributes title=""/>
+      <privatestaticattributes title=""/>
+      <friends title=""/>
+      <related title="" subtitle=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <services title=""/>
+      <interfaces title=""/>
+      <constructors title=""/>
+      <functions title=""/>
+      <related title=""/>
+      <variables title=""/>
+      <properties title=""/>
+      <events title=""/>
+    </memberdef>
+    <allmemberslink visible="yes"/>
+    <usedfiles visible="$SHOW_USED_FILES"/>
+    <authorsection visible="yes"/>
+  </class>
+
+  <!-- Layout definition for a namespace page -->
+  <namespace>
+    <briefdescription visible="yes"/>
+    <memberdecl>
+      <nestednamespaces visible="yes" title=""/>
+      <constantgroups visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </namespace>
+
+  <!-- Layout definition for a file page -->
+  <file>
+    <briefdescription visible="yes"/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <includegraph visible="$INCLUDE_GRAPH"/>
+    <includedbygraph visible="$INCLUDED_BY_GRAPH"/>
+    <sourcelink visible="yes"/>
+    <memberdecl>
+      <classes visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <constantgroups visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection/>
+  </file>
+
+  <!-- Layout definition for a group page -->
+  <group>
+    <briefdescription visible="yes"/>
+    <groupgraph visible="$GROUP_GRAPHS"/>
+    <memberdecl>
+      <nestedgroups visible="yes" title=""/>
+      <dirs visible="yes" title=""/>
+      <files visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <pagedocs/>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </group>
+
+  <!-- Layout definition for a directory page -->
+  <directory>
+    <briefdescription visible="yes"/>
+    <directorygraph visible="yes"/>
+    <memberdecl>
+      <dirs visible="yes"/>
+      <files visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+  </directory>
+</doxygenlayout>