Steffen Möller · Steffen Möller · Steffen Möller · Steffen Möller · 8ed8db38 · 8ed8db38
--- a/AUTHORS
+++ b/AUTHORS
@@ -5,7 +5,6 @@ md5 code in src/libmaus2/digest/md5.[ch] by L. Peter Deutsch (Aladdin Enterprise
 some code in src/libmaus2/bambam/DuplicationMetrics.hpp is imported from the Picard project (MIT license, see file for copyright)
 LZ4 code in src/libmaus2/lz/lz4.[ch] by Yann Collect (BSD 2-Clause licence, see files)
 CRC32 code in src/libmaus2/hashing/Crc3.{cpp/hpp} by Stephan Brumme (ZLib type license, see files)
-libmaus2/digest/sha(256|512)_*.asm (Intel license, see files)
 Part of CRC32{|C} code in src/libmaus2/digest/CRC32{|C}_Core.cpp by Mark Adler (see file for license)
 Hash code in src/libmaus2/hashing/MurmurHash3.{cpp|h} and libmaus2/digest/MurmurHash3_x64_128.hpp by Austin Appleby (public domain)
 Rest by German Tischler published under GPLv2/GPLv3 (some of it written while at Genome Research Limited/WTSI)
--- a/ChangeLog
+++ b/ChangeLog
+libmaus2 (2.0.684-1) unstable; urgency=medium
+
+  * add reset method in IndexBase
+  * add cast in RangeSet
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Mon, 04 Nov 2019 10:53:24 +0100
+
+libmaus2 (2.0.683-1) unstable; urgency=medium
+
+  * fix LineSplitting output stream buffer for case only one file gets created (do not erroneously remove file on the wrong assumption it is empty)
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 30 Oct 2019 10:28:03 +0100
+
+libmaus2 (2.0.682-1) unstable; urgency=medium
+
+  * guard against flush exceptions in BamToFastqOutputFileSet destructor
+  * add separate flush function in BamToFastqOutputFileSet
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 30 Oct 2019 09:14:28 +0100
+
+libmaus2 (2.0.681-1) unstable; urgency=medium
+
+  * replace assert statements by exceptions in TabEntry
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 25 Oct 2019 10:00:14 +0200
+
+libmaus2 (2.0.680-1) unstable; urgency=medium
+
+  * add filename based constructor in VEPParser
+  * add getParsed method in TabEntry
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 23 Oct 2019 15:24:01 +0200
+
+libmaus2 (2.0.679-1) unstable; urgency=medium
+
+  * add reverse method in Distribution
+  * add HistogramBuckets class
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 22 Oct 2019 14:09:22 +0200
+
+libmaus2 (2.0.678-1) unstable; urgency=medium
+
+  * add Distribution class
+  * add NormalDistribution and LogNormalDistribution classes
+  * use ::std::erf instead of custom implementation
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Mon, 21 Oct 2019 15:15:06 +0200
+
+libmaus2 (2.0.677-1) unstable; urgency=medium
+
+  * add getContigNamesAndTrie in BamHeader
+  * add getPileQualityVector function/method in BamAlignmentDecoderBase/BamAlignment
+  * fix namespace scope of output operator for ArgInfo
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Mon, 21 Oct 2019 08:04:46 +0200
+
+libmaus2 (2.0.676-1) unstable; urgency=medium
+
+  * support end of range queries in PosMapping class
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 11 Oct 2019 10:13:48 +0200
+
+libmaus2 (2.0.675-1) unstable; urgency=medium
+
+  * add VEPParser class
+  * fix bug in VCFParser dropping the first data line after the VCF header
+  * add VEPCoordinate class
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 10 Oct 2019 15:03:01 +0200
+
+libmaus2 (2.0.674-1) unstable; urgency=medium
+
+  * add commonPrefix function in stringFunctions class
+  * add VCFParser constructor taking file name argument
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 09 Oct 2019 13:35:19 +0200
+
+libmaus2 (2.0.673-1) unstable; urgency=medium
+
+  * simplify configure script
+  * code cleanup (remove fftw and daligner code dependencies)
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 09 Oct 2019 10:21:25 +0200
+
+libmaus2 (2.0.672-1) unstable; urgency=medium
+
+  * add peek/read methods in VCFParser
+  * add getCoordinate function in VCFParser
+  * add VCFSorter class
+  * add getContigNamesAndTrie function/method in VCFParser
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 08 Oct 2019 10:35:25 +0200
+
+libmaus2 (2.0.671-1) unstable; urgency=medium
+
+  * fix errors after removal of assembly based digest functions
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 03 Oct 2019 20:11:42 +0200
+
+libmaus2 (2.0.670-1) unstable; urgency=medium
+
+  * remove assembly code for digests/hashs
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 27 Sep 2019 11:09:46 +0200
+
+libmaus2 (2.0.669-1) unstable; urgency=medium
+
+  * add seed position based alignment in Align
+  * remove erroneous assert statements in Align class
+  * add extendedLF in LFBase class
+  * add phi function for BiInterval in FM class
+  * add loading of WaveletTree based LF in BwtMergeSortResult
+  * add FM::BiInterval class inside FM and helper functions (epsilon,extendLeft,extendRight)
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 24 Sep 2019 12:56:20 +0200
+
+libmaus2 (2.0.668-1) unstable; urgency=medium
+
+  * add simple protein alignment class
+  * add blosum62
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 19 Sep 2019 21:43:44 +0200
+
+libmaus2 (2.0.667-1) unstable; urgency=medium
+
+  * add constructor by file name in LineBuffer class
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 18 Sep 2019 09:37:03 +0200
+
+libmaus2 (2.0.666-1) unstable; urgency=medium
+
+  * allow initialisation by pseudo BED data in GTFData object
+  * allow construction via vector instead of GTFData in BAMGTFMap
+  * add GeneRangeSets and TranscriptRangeSets classes
+  * fill id field for Gene in GTFData
+  * add getFrom(), getTo() and getInterval() methods in Gene
+  * add getFrom(), getTo() and getInterval() methods in Transcript
+  * store length value in RangeSet and replace several assert statements by exceptions
+  * add filter method in GTFData
+  * add c_start, c_end and id attributes in Transcript
+  * add strand attribute in CDS
+  * remove debug message in GTFData
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 05 Sep 2019 15:12:09 +0200
+
+libmaus2 (2.0.665-1) unstable; urgency=medium
+
+  * add RangeSets class in gtf
+  * add BAMGTFMap class
+  * add sanity checking code in GTFData
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 29 Aug 2019 17:12:56 +0200
+
+libmaus2 (2.0.664-1) unstable; urgency=medium
+
+  * add code for analysing/handling GTF files
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 29 Aug 2019 11:20:29 +0200
+
 libmaus2 (2.0.663-1) unstable; urgency=medium

  * allow registering files as temp files in SerialisingSortingBufferedOutputFileArray

--- a/Makefile.am
+++ b/Makefile.am
@@ -3,7 +3,7 @@ SUBDIRS = src @TESTDIR@
 ACLOCAL_AMFLAGS=-I m4

 pkgconfigdir = $(libdir)/pkgconfig
-pkgconfig_DATA = libmaus2.pc libmaus2digests.pc libmaus2seqchksumsfactory.pc libmaus2fftw.pc @LIBMAUSIRODSPC@
+pkgconfig_DATA = libmaus2.pc @LIBMAUSIRODSPC@

 doc_DATA = ChangeLog


--- a/Makefile.in
+++ b/Makefile.in
@@ -103,8 +103,7 @@ am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
 configure.lineno config.status.lineno
 mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = config.h
-CONFIG_CLEAN_FILES = libmaus2.pc libmaus2digests.pc libmaus2irods.pc \
-	libmaus2seqchksumsfactory.pc libmaus2fftw.pc ubuntu.sh \
+CONFIG_CLEAN_FILES = libmaus2.pc libmaus2irods.pc ubuntu.sh \
 	src/libmaus2/LibMausConfig.hpp
 CONFIG_CLEAN_VPATH_FILES =
 AM_V_P = $(am__v_P_@AM_V@)
@@ -194,9 +193,7 @@ CTAGS = ctags
 CSCOPE = cscope
 DIST_SUBDIRS = $(SUBDIRS)
 am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/config.h.in \
-	$(srcdir)/libmaus2.pc.in $(srcdir)/libmaus2digests.pc.in \
-	$(srcdir)/libmaus2fftw.pc.in $(srcdir)/libmaus2irods.pc.in \
-	$(srcdir)/libmaus2seqchksumsfactory.pc.in \
+	$(srcdir)/libmaus2.pc.in $(srcdir)/libmaus2irods.pc.in \
 	$(srcdir)/ubuntu.sh.in \
 	$(top_srcdir)/src/libmaus2/LibMausConfig.hpp.in AUTHORS \
 	COPYING ChangeLog INSTALL NEWS README compile config.guess \
@@ -258,19 +255,13 @@ CCDEPMODE = @CCDEPMODE@
 CFLAGS = @CFLAGS@
 CPP = @CPP@
 CPPFLAGS = @CPPFLAGS@
-CSTDINT = @CSTDINT@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
 CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
-DALIGNERCPPFLAGS = @DALIGNERCPPFLAGS@
-DALIGNERLDFLAGS = @DALIGNERLDFLAGS@
-DALIGNERLIBS = @DALIGNERLIBS@
 DEFS = @DEFS@
 DEPDIR = @DEPDIR@
-DIGESTASMOBJ = @DIGESTASMOBJ@
-DLFUNCS = @DLFUNCS@
 DLLIB = @DLLIB@
 DLLTOOL = @DLLTOOL@
 DSYMUTIL = @DSYMUTIL@
@@ -279,66 +270,16 @@ ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
 EGREP = @EGREP@
-ENDIANESS = @ENDIANESS@
 EXEEXT = @EXEEXT@
-FCNTL_H = @FCNTL_H@
-FFTWCPPFLAGS = @FFTWCPPFLAGS@
-FFTWLDFLAGS = @FFTWLDFLAGS@
-FFTWLIBS = @FFTWLIBS@
 FGREP = @FGREP@
-FILTERRELATIONMATRIX = @FILTERRELATIONMATRIX@
 GMPCPPFLAGS = @GMPCPPFLAGS@
 GMPLDFLAGS = @GMPLDFLAGS@
 GMPLIBS = @GMPLIBS@
-GNUTLS = @GNUTLS@
 GNUTLSCPPFLAGS = @GNUTLSCPPFLAGS@
 GNUTLSLDFLAGS = @GNUTLSLDFLAGS@
 GNUTLSLIBS = @GNUTLSLIBS@
 GNUTLSREQ = @GNUTLSREQ@
 GREP = @GREP@
-HAVEARPAINETH = @HAVEARPAINETH@
-HAVEBACKTRACE = @HAVEBACKTRACE@
-HAVEDARWINSPINLOCKS = @HAVEDARWINSPINLOCKS@
-HAVEDLFCNH = @HAVEDLFCNH@
-HAVEGETPAGESIZE = @HAVEGETPAGESIZE@
-HAVEHAVEFEATURESH = @HAVEHAVEFEATURESH@
-HAVEI386 = @HAVEI386@
-HAVELINUXSYSCTLH = @HAVELINUXSYSCTLH@
-HAVEMSGCMSGCLOEXEC = @HAVEMSGCMSGCLOEXEC@
-HAVENETDBH = @HAVENETDBH@
-HAVENETINETINH = @HAVENETINETINH@
-HAVENETINETTCPH = @HAVENETINETTCPH@
-HAVEPOLLH = @HAVEPOLLH@
-HAVEPOSIXMEMALIGN = @HAVEPOSIXMEMALIGN@
-HAVEPRCTL = @HAVEPRCTL@
-HAVEPTHREADATTRSETAFFINITYNP = @HAVEPTHREADATTRSETAFFINITYNP@
-HAVEPTHREADGETNAME_NP = @HAVEPTHREADGETNAME_NP@
-HAVEPTHREADGET_NAME_NP = @HAVEPTHREADGET_NAME_NP@
-HAVEPTHREADS = @HAVEPTHREADS@
-HAVEPTHREADSETAFFINITYNP = @HAVEPTHREADSETAFFINITYNP@
-HAVEPTHREADSETNAME_NP = @HAVEPTHREADSETNAME_NP@
-HAVEPTHREADSET_NAME_NP = @HAVEPTHREADSET_NAME_NP@
-HAVESEMDESTROY = @HAVESEMDESTROY@
-HAVESEMINIT = @HAVESEMINIT@
-HAVESEMPOST = @HAVESEMPOST@
-HAVESEMTIMEDWAIT = @HAVESEMTIMEDWAIT@
-HAVESEMWAIT = @HAVESEMWAIT@
-HAVESETRLIMIT = @HAVESETRLIMIT@
-HAVESETSOCKOPT = @HAVESETSOCKOPT@
-HAVESMMINTRINH = @HAVESMMINTRINH@
-HAVESSE4 = @HAVESSE4@
-HAVESSSE3 = @HAVESSSE3@
-HAVESTDINTH = @HAVESTDINTH@
-HAVESYNCLOCK = @HAVESYNCLOCK@
-HAVESYNCOPS = @HAVESYNCOPS@
-HAVESYSIOCTLH = @HAVESYSIOCTLH@
-HAVESYSRESOURCEH = @HAVESYSRESOURCEH@
-HAVESYSSOCKETH = @HAVESYSSOCKETH@
-HAVESYSVFSH = @HAVESYSVFSH@
-HAVEUNISTDH = @HAVEUNISTDH@
-HAVEUNSIGNEDINT128 = @HAVEUNSIGNEDINT128@
-HAVEWINDOWSH = @HAVEWINDOWSH@
-HAVEX8664 = @HAVEX8664@
 IGZIPCPPFLAGS = @IGZIPCPPFLAGS@
 IGZIPLDFLAGS = @IGZIPLDFLAGS@
 IGZIPLIBS = @IGZIPLIBS@
@@ -347,13 +288,9 @@ INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
 INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-IOLIBCALLBACKDEFINE = @IOLIBCALLBACKDEFINE@
 IOLIBCPPFLAGS = @IOLIBCPPFLAGS@
-IOLIBDEFINE = @IOLIBDEFINE@
-IOLIBINDEXCALLBACKDEFINE = @IOLIBINDEXCALLBACKDEFINE@
 IOLIBLDFLAGS = @IOLIBLDFLAGS@
 IOLIBLIBS = @IOLIBLIBS@
-IOLIBNEWINTERFACEDEFINE = @IOLIBNEWINTERFACEDEFINE@
 IO_LIB_CONFIG = @IO_LIB_CONFIG@
 IRODSCPPFLAGS = @IRODSCPPFLAGS@
 IRODSCXXFLAGS = @IRODSCXXFLAGS@
@@ -366,21 +303,26 @@ LIBDEFLATECPPFLAGS = @LIBDEFLATECPPFLAGS@
 LIBDEFLATECXXFLAGS = @LIBDEFLATECXXFLAGS@
 LIBDEFLATELDFLAGS = @LIBDEFLATELDFLAGS@
 LIBDEFLATELIBS = @LIBDEFLATELIBS@
-LIBGEN_H = @LIBGEN_H@
 LIBMAUS2_AUTOARRAY_AUTOARRAYTRACE = @LIBMAUS2_AUTOARRAY_AUTOARRAYTRACE@
 LIBMAUS2_DEBUG_COMPILED = @LIBMAUS2_DEBUG_COMPILED@
 LIBMAUS2_ENABLE_RTLD_DEEPBIND = @LIBMAUS2_ENABLE_RTLD_DEEPBIND@
+LIBMAUS2_ENDIANESS = @LIBMAUS2_ENDIANESS@
 LIBMAUS2_FILEOFFSET_BITS = @LIBMAUS2_FILEOFFSET_BITS@
 LIBMAUS2_HAVE_ALIGNMENT_ONE_TO_MANY_AVX2 = @LIBMAUS2_HAVE_ALIGNMENT_ONE_TO_MANY_AVX2@
+LIBMAUS2_HAVE_ARPA_INET_H = @LIBMAUS2_HAVE_ARPA_INET_H@
 LIBMAUS2_HAVE_AVX = @LIBMAUS2_HAVE_AVX@
 LIBMAUS2_HAVE_AVX2 = @LIBMAUS2_HAVE_AVX2@
+LIBMAUS2_HAVE_BACKTRACE = @LIBMAUS2_HAVE_BACKTRACE@
 LIBMAUS2_HAVE_BASENAME = @LIBMAUS2_HAVE_BASENAME@
 LIBMAUS2_HAVE_CLOSE = @LIBMAUS2_HAVE_CLOSE@
-LIBMAUS2_HAVE_DALIGNER = @LIBMAUS2_HAVE_DALIGNER@
+LIBMAUS2_HAVE_CSTDINT = @LIBMAUS2_HAVE_CSTDINT@
 LIBMAUS2_HAVE_DIRNAME = @LIBMAUS2_HAVE_DIRNAME@
+LIBMAUS2_HAVE_DLFCN_H = @LIBMAUS2_HAVE_DLFCN_H@
+LIBMAUS2_HAVE_DLFUNCS = @LIBMAUS2_HAVE_DLFUNCS@
 LIBMAUS2_HAVE_EXECINFO_H = @LIBMAUS2_HAVE_EXECINFO_H@
 LIBMAUS2_HAVE_FCNTL = @LIBMAUS2_HAVE_FCNTL@
-LIBMAUS2_HAVE_FFTW = @LIBMAUS2_HAVE_FFTW@
+LIBMAUS2_HAVE_FCNTL_H = @LIBMAUS2_HAVE_FCNTL_H@
+LIBMAUS2_HAVE_FEATURES_H = @LIBMAUS2_HAVE_FEATURES_H@
 LIBMAUS2_HAVE_FORK = @LIBMAUS2_HAVE_FORK@
 LIBMAUS2_HAVE_FSTAT = @LIBMAUS2_HAVE_FSTAT@
 LIBMAUS2_HAVE_FSTATFS = @LIBMAUS2_HAVE_FSTATFS@
@@ -388,19 +330,36 @@ LIBMAUS2_HAVE_FSYNC = @LIBMAUS2_HAVE_FSYNC@
 LIBMAUS2_HAVE_GETADDRINFO = @LIBMAUS2_HAVE_GETADDRINFO@
 LIBMAUS2_HAVE_GETHOSTBYNAME = @LIBMAUS2_HAVE_GETHOSTBYNAME@
 LIBMAUS2_HAVE_GETHOSTBYNAME2 = @LIBMAUS2_HAVE_GETHOSTBYNAME2@
+LIBMAUS2_HAVE_GETPAGESIZE = @LIBMAUS2_HAVE_GETPAGESIZE@
 LIBMAUS2_HAVE_GETPID = @LIBMAUS2_HAVE_GETPID@
 LIBMAUS2_HAVE_GLOBAL_ALIGNMENT_X128_16 = @LIBMAUS2_HAVE_GLOBAL_ALIGNMENT_X128_16@
 LIBMAUS2_HAVE_GLOBAL_ALIGNMENT_X128_8 = @LIBMAUS2_HAVE_GLOBAL_ALIGNMENT_X128_8@
 LIBMAUS2_HAVE_GLOBAL_ALIGNMENT_Y256_16 = @LIBMAUS2_HAVE_GLOBAL_ALIGNMENT_Y256_16@
 LIBMAUS2_HAVE_GLOBAL_ALIGNMENT_Y256_8 = @LIBMAUS2_HAVE_GLOBAL_ALIGNMENT_Y256_8@
 LIBMAUS2_HAVE_GMP = @LIBMAUS2_HAVE_GMP@
+LIBMAUS2_HAVE_GNUTLS = @LIBMAUS2_HAVE_GNUTLS@
 LIBMAUS2_HAVE_HSTRERROR = @LIBMAUS2_HAVE_HSTRERROR@
+LIBMAUS2_HAVE_I386 = @LIBMAUS2_HAVE_I386@
 LIBMAUS2_HAVE_IGZIP = @LIBMAUS2_HAVE_IGZIP@
+LIBMAUS2_HAVE_IOLIB = @LIBMAUS2_HAVE_IOLIB@
+LIBMAUS2_HAVE_IO_LIB_INPUT_CALLBACKS = @LIBMAUS2_HAVE_IO_LIB_INPUT_CALLBACKS@
+LIBMAUS2_HAVE_IO_LIB_INPUT_INDEX_CALLBACKS = @LIBMAUS2_HAVE_IO_LIB_INPUT_INDEX_CALLBACKS@
+LIBMAUS2_HAVE_IO_NEW_CRAM_INTERFACE = @LIBMAUS2_HAVE_IO_NEW_CRAM_INTERFACE@
 LIBMAUS2_HAVE_IRODS = @LIBMAUS2_HAVE_IRODS@
+LIBMAUS2_HAVE_LIBDEFLATE = @LIBMAUS2_HAVE_LIBDEFLATE@
+LIBMAUS2_HAVE_LIBGEN_H = @LIBMAUS2_HAVE_LIBGEN_H@
+LIBMAUS2_HAVE_LINUX_SYSCTL_H = @LIBMAUS2_HAVE_LINUX_SYSCTL_H@
 LIBMAUS2_HAVE_LSEEK = @LIBMAUS2_HAVE_LSEEK@
 LIBMAUS2_HAVE_LZMA = @LIBMAUS2_HAVE_LZMA@
+LIBMAUS2_HAVE_MKDIR_ONE_ARG = @LIBMAUS2_HAVE_MKDIR_ONE_ARG@
+LIBMAUS2_HAVE_MKDIR_TWO_ARGS = @LIBMAUS2_HAVE_MKDIR_TWO_ARGS@
 LIBMAUS2_HAVE_MMAP = @LIBMAUS2_HAVE_MMAP@
 LIBMAUS2_HAVE_MMAP_HUGEPAGES = @LIBMAUS2_HAVE_MMAP_HUGEPAGES@
+LIBMAUS2_HAVE_MOVE_FUNC = @LIBMAUS2_HAVE_MOVE_FUNC@
+LIBMAUS2_HAVE_NETDB_H = @LIBMAUS2_HAVE_NETDB_H@
+LIBMAUS2_HAVE_NETINET_IN_H = @LIBMAUS2_HAVE_NETINET_IN_H@
+LIBMAUS2_HAVE_NETINET_TCP_H = @LIBMAUS2_HAVE_NETINET_TCP_H@
+LIBMAUS2_HAVE_NETTLE = @LIBMAUS2_HAVE_NETTLE@
 LIBMAUS2_HAVE_OFF_T = @LIBMAUS2_HAVE_OFF_T@
 LIBMAUS2_HAVE_OPEN_2 = @LIBMAUS2_HAVE_OPEN_2@
 LIBMAUS2_HAVE_OPEN_3 = @LIBMAUS2_HAVE_OPEN_3@
@@ -413,41 +372,64 @@ LIBMAUS2_HAVE_O_TRUNC = @LIBMAUS2_HAVE_O_TRUNC@
 LIBMAUS2_HAVE_O_WRONLY = @LIBMAUS2_HAVE_O_WRONLY@
 LIBMAUS2_HAVE_PID_T = @LIBMAUS2_HAVE_PID_T@
 LIBMAUS2_HAVE_PIPE = @LIBMAUS2_HAVE_PIPE@
+LIBMAUS2_HAVE_POLL_H = @LIBMAUS2_HAVE_POLL_H@
+LIBMAUS2_HAVE_POSIXMEMALIGN = @LIBMAUS2_HAVE_POSIXMEMALIGN@
+LIBMAUS2_HAVE_PRCTL = @LIBMAUS2_HAVE_PRCTL@
+LIBMAUS2_HAVE_PTHREADS = @LIBMAUS2_HAVE_PTHREADS@
 LIBMAUS2_HAVE_READ = @LIBMAUS2_HAVE_READ@
-LIBMAUS2_HAVE_SHA2_ASSEMBLY = @LIBMAUS2_HAVE_SHA2_ASSEMBLY@
+LIBMAUS2_HAVE_SETRLIMIT = @LIBMAUS2_HAVE_SETRLIMIT@
+LIBMAUS2_HAVE_SETSOCKOPT = @LIBMAUS2_HAVE_SETSOCKOPT@
+LIBMAUS2_HAVE_SHARED_PTR = @LIBMAUS2_HAVE_SHARED_PTR@
 LIBMAUS2_HAVE_SIGHUP = @LIBMAUS2_HAVE_SIGHUP@
 LIBMAUS2_HAVE_SIGPIPE = @LIBMAUS2_HAVE_SIGPIPE@
+LIBMAUS2_HAVE_SMMINTRIN_H = @LIBMAUS2_HAVE_SMMINTRIN_H@
+LIBMAUS2_HAVE_SNAPPY = @LIBMAUS2_HAVE_SNAPPY@
 LIBMAUS2_HAVE_SOCKLEN_T = @LIBMAUS2_HAVE_SOCKLEN_T@
+LIBMAUS2_HAVE_SSE4 = @LIBMAUS2_HAVE_SSE4@
 LIBMAUS2_HAVE_SSIZE_T = @LIBMAUS2_HAVE_SSIZE_T@
+LIBMAUS2_HAVE_SSSE3 = @LIBMAUS2_HAVE_SSSE3@
 LIBMAUS2_HAVE_STAT = @LIBMAUS2_HAVE_STAT@
 LIBMAUS2_HAVE_STATFS = @LIBMAUS2_HAVE_STATFS@
 LIBMAUS2_HAVE_STATFS_F_BSIZE = @LIBMAUS2_HAVE_STATFS_F_BSIZE@
 LIBMAUS2_HAVE_STATFS_F_IOSIZE = @LIBMAUS2_HAVE_STATFS_F_IOSIZE@
+LIBMAUS2_HAVE_STDINT_H = @LIBMAUS2_HAVE_STDINT_H@
 LIBMAUS2_HAVE_SYMLINK = @LIBMAUS2_HAVE_SYMLINK@
+LIBMAUS2_HAVE_SYNC_OPS = @LIBMAUS2_HAVE_SYNC_OPS@
 LIBMAUS2_HAVE_SYSCONF = @LIBMAUS2_HAVE_SYSCONF@
+LIBMAUS2_HAVE_SYS_IOCTL_H = @LIBMAUS2_HAVE_SYS_IOCTL_H@
+LIBMAUS2_HAVE_SYS_PRCTL_H = @LIBMAUS2_HAVE_SYS_PRCTL_H@
+LIBMAUS2_HAVE_SYS_RESOURCE_H = @LIBMAUS2_HAVE_SYS_RESOURCE_H@
 LIBMAUS2_HAVE_SYS_SELECT_H = @LIBMAUS2_HAVE_SYS_SELECT_H@
+LIBMAUS2_HAVE_SYS_SOCKET_H = @LIBMAUS2_HAVE_SYS_SOCKET_H@
+LIBMAUS2_HAVE_SYS_STAT_H = @LIBMAUS2_HAVE_SYS_STAT_H@
+LIBMAUS2_HAVE_SYS_TIME_H = @LIBMAUS2_HAVE_SYS_TIME_H@
+LIBMAUS2_HAVE_SYS_TYPES_H = @LIBMAUS2_HAVE_SYS_TYPES_H@
+LIBMAUS2_HAVE_SYS_VFS_H = @LIBMAUS2_HAVE_SYS_VFS_H@
 LIBMAUS2_HAVE_SYS_WAIT_H = @LIBMAUS2_HAVE_SYS_WAIT_H@
-LIBMAUS2_HAVE_VFS_H = @LIBMAUS2_HAVE_VFS_H@
+LIBMAUS2_HAVE_UNIQUE_PTR = @LIBMAUS2_HAVE_UNIQUE_PTR@
+LIBMAUS2_HAVE_UNISTD_H = @LIBMAUS2_HAVE_UNISTD_H@
+LIBMAUS2_HAVE_UNORDERED_MAP = @LIBMAUS2_HAVE_UNORDERED_MAP@
+LIBMAUS2_HAVE_UNORDERED_SET = @LIBMAUS2_HAVE_UNORDERED_SET@
+LIBMAUS2_HAVE_UNSIGNED_INT_128 = @LIBMAUS2_HAVE_UNSIGNED_INT_128@
 LIBMAUS2_HAVE_WAITPID = @LIBMAUS2_HAVE_WAITPID@
 LIBMAUS2_HAVE_WEXITSTATUS = @LIBMAUS2_HAVE_WEXITSTATUS@
 LIBMAUS2_HAVE_WIFEXITED = @LIBMAUS2_HAVE_WIFEXITED@
+LIBMAUS2_HAVE_WINDOWS_H = @LIBMAUS2_HAVE_WINDOWS_H@
 LIBMAUS2_HAVE_WINSOCK2_H = @LIBMAUS2_HAVE_WINSOCK2_H@
 LIBMAUS2_HAVE_WRITE = @LIBMAUS2_HAVE_WRITE@
 LIBMAUS2_HAVE_WS2TCPIP_H = @LIBMAUS2_HAVE_WS2TCPIP_H@
+LIBMAUS2_HAVE_X86_64 = @LIBMAUS2_HAVE_X86_64@
 LIBMAUS2_IRODS_NEED_PREFIX = @LIBMAUS2_IRODS_NEED_PREFIX@
 LIBMAUS2_LARGEFILE_SOURCE = @LIBMAUS2_LARGEFILE_SOURCE@
 LIBMAUS2_LZMA_CPPFLAGS = @LIBMAUS2_LZMA_CPPFLAGS@
 LIBMAUS2_LZMA_LIBS = @LIBMAUS2_LZMA_LIBS@
 LIBMAUS2_LZMA_REQ = @LIBMAUS2_LZMA_REQ@
-LIBMAUS2_MKDIR_ONE_ARG = @LIBMAUS2_MKDIR_ONE_ARG@
-LIBMAUS2_MKDIR_TWO_ARGS = @LIBMAUS2_MKDIR_TWO_ARGS@
 LIBMAUS2_NETTLE_HAVE_SHA3 = @LIBMAUS2_NETTLE_HAVE_SHA3@
 LIBMAUS2_SIZEOF_UNSIGNED_LONG = @LIBMAUS2_SIZEOF_UNSIGNED_LONG@
+LIBMAUS2_USE_ASSEMBLY = @LIBMAUS2_USE_ASSEMBLY@
 LIBMAUSARCHCFLAGS = @LIBMAUSARCHCFLAGS@
 LIBMAUSCPPFLAGS = @LIBMAUSCPPFLAGS@
 LIBMAUSCXXFLAGS = @LIBMAUSCXXFLAGS@
-LIBMAUSHAVELIBDEFLATE = @LIBMAUSHAVELIBDEFLATE@
-LIBMAUSHAVESNAPPY = @LIBMAUSHAVESNAPPY@
 LIBMAUSIRODSPC = @LIBMAUSIRODSPC@
 LIBMAUSLDFLAGS = @LIBMAUSLDFLAGS@
 LIBMAUSLIBS = @LIBMAUSLIBS@
@@ -467,12 +449,10 @@ MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
 MAVX2 = @MAVX2@
 MKDIR_P = @MKDIR_P@
-MOVEFUNC = @MOVEFUNC@
 MSSE2 = @MSSE2@
 MSSE4 = @MSSE4@
 MSSE41 = @MSSE41@
 MSSSE3 = @MSSSE3@
-NETTLE = @NETTLE@
 NETTLECPPFLAGS = @NETTLECPPFLAGS@
 NETTLELDFLAGS = @NETTLELDFLAGS@
 NETTLELIBS = @NETTLELIBS@
@@ -495,35 +475,19 @@ PKGSSE4 = @PKGSSE4@
 PKG_CONFIG = @PKG_CONFIG@
 PKG_CONFIG_LIBDIR = @PKG_CONFIG_LIBDIR@
 PKG_CONFIG_PATH = @PKG_CONFIG_PATH@
-POSIXSPINLOCKS = @POSIXSPINLOCKS@
 RANLIB = @RANLIB@
-REGEXH = @REGEXH@
-SDSLCPPFLAGS = @SDSLCPPFLAGS@
-SDSLCXXFLAGS = @SDSLCXXFLAGS@
-SDSLLIBS = @SDSLLIBS@
 SED = @SED@
 SET_MAKE = @SET_MAKE@
-SHAREDPTR = @SHAREDPTR@
 SHELL = @SHELL@
 SNAPPYCPPFLAGS = @SNAPPYCPPFLAGS@
 SNAPPYCXXFLAGS = @SNAPPYCXXFLAGS@
 SNAPPYLDFLAGS = @SNAPPYLDFLAGS@
 SNAPPYLIBS = @SNAPPYLIBS@
 STRIP = @STRIP@
-SYSTIMEH = @SYSTIMEH@
-SYS_STAT_H = @SYS_STAT_H@
-SYS_TYPES_H = @SYS_TYPES_H@
-SYS_VFS_H = @SYS_VFS_H@
 TESTDIR = @TESTDIR@
 TESTPROGS = @TESTPROGS@
-UNIQUEPTR = @UNIQUEPTR@
-UNORDEREDMAP = @UNORDEREDMAP@
-UNORDEREDSET = @UNORDEREDSET@
-USEASSEMBLY = @USEASSEMBLY@
 VERSION = @VERSION@
 WARNCXXFLAGS = @WARNCXXFLAGS@
-WINDOWSH = @WINDOWSH@
-YASMEXE = @YASMEXE@
 ZLIBCPPFLAGS = @ZLIBCPPFLAGS@
 ZLIBCXXFLAGS = @ZLIBCXXFLAGS@
 ZLIBLIBS = @ZLIBLIBS@
@@ -553,8 +517,6 @@ datarootdir = @datarootdir@
 docdir = @docdir@
 dvidir = @dvidir@
 exec_prefix = @exec_prefix@
-fftw3_CFLAGS = @fftw3_CFLAGS@
-fftw3_LIBS = @fftw3_LIBS@
 gnutls_CFLAGS = @gnutls_CFLAGS@
 gnutls_LIBS = @gnutls_LIBS@
 host = @host@
@@ -600,7 +562,7 @@ EXTRA_DIST = configure GPLv2 GPLv3
 SUBDIRS = src @TESTDIR@
 ACLOCAL_AMFLAGS = -I m4
 pkgconfigdir = $(libdir)/pkgconfig
-pkgconfig_DATA = libmaus2.pc libmaus2digests.pc libmaus2seqchksumsfactory.pc libmaus2fftw.pc @LIBMAUSIRODSPC@
+pkgconfig_DATA = libmaus2.pc @LIBMAUSIRODSPC@
 doc_DATA = ChangeLog
 all: config.h
 	$(MAKE) $(AM_MAKEFLAGS) all-recursive
@@ -656,14 +618,8 @@ distclean-hdr:
 	-rm -f config.h stamp-h1
 libmaus2.pc: $(top_builddir)/config.status $(srcdir)/libmaus2.pc.in
 	cd $(top_builddir) && $(SHELL) ./config.status $@
-libmaus2digests.pc: $(top_builddir)/config.status $(srcdir)/libmaus2digests.pc.in
-	cd $(top_builddir) && $(SHELL) ./config.status $@
 libmaus2irods.pc: $(top_builddir)/config.status $(srcdir)/libmaus2irods.pc.in
 	cd $(top_builddir) && $(SHELL) ./config.status $@
-libmaus2seqchksumsfactory.pc: $(top_builddir)/config.status $(srcdir)/libmaus2seqchksumsfactory.pc.in
-	cd $(top_builddir) && $(SHELL) ./config.status $@
-libmaus2fftw.pc: $(top_builddir)/config.status $(srcdir)/libmaus2fftw.pc.in
-	cd $(top_builddir) && $(SHELL) ./config.status $@
 ubuntu.sh: $(top_builddir)/config.status $(srcdir)/ubuntu.sh.in
 	cd $(top_builddir) && $(SHELL) ./config.status $@
 src/libmaus2/LibMausConfig.hpp: $(top_builddir)/config.status $(top_srcdir)/src/libmaus2/LibMausConfig.hpp.in

--- a/autom4te.cache/output.0
+++ b/autom4te.cache/output.0
--- a/autom4te.cache/output.1
+++ b/autom4te.cache/output.1
--- a/autom4te.cache/output.2
+++ b/autom4te.cache/output.2
--- a/autom4te.cache/requests
+++ b/autom4te.cache/requests
--- a/autom4te.cache/traces.0
+++ b/autom4te.cache/traces.0
--- a/autom4te.cache/traces.1
+++ b/autom4te.cache/traces.1
--- a/autom4te.cache/traces.2
+++ b/autom4te.cache/traces.2
--- a/configure
+++ b/configure
--- a/configure.ac
+++ b/configure.ac
--- a/debian/changelog
+++ b/debian/changelog
+libmaus2 (2.0.684-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+
+ -- Steffen Moeller <moeller@debian.org>  Wed, 06 Nov 2019 14:51:15 +0100
+
 libmaus2 (2.0.663-1) unstable; urgency=medium

  * Team upload.

--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 12),
               d-shlibs,
               pkg-config,
               zlib1g-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 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

--- a/libmaus2digests.pc.in
+++ b/libmaus2digests.pc.in
-prefix=@prefix@
-exec_prefix=@exec_prefix@
-libdir=@libdir@
-includedir=@includedir@
-
-Name: libmaus2digests
-Description: non pic digest routines in libmaus2
-Requires: @ZLIBREQ@ @NETTLEREQ@
-Version: @VERSION@
-Libs: -L${libdir} -lmaus2digests -lmaus2digests_sse4
-Cflags: @LIBMAUSCPPFLAGS@ @LIBMAUSPKGCPPFLAGS@ @LIBMAUSPKGCXXFLAGS@ @LIBMAUSARCHCFLAGS@ @ZLIBCPPFLAGS@ -I${includedir}
--- a/libmaus2fftw.pc.in
+++ b/libmaus2fftw.pc.in
-prefix=@prefix@
-exec_prefix=@exec_prefix@
-libdir=@libdir@
-includedir=@includedir@
-
-Name: libmaus2fftw
-Description: non pic fftw based routines in libmaus2
-Requires:
-Version: @VERSION@
-Libs: -L${libdir} -lmaus2fftw @FFTWLIBS@
-Cflags: @LIBMAUSCPPFLAGS@ @LIBMAUSPKGCPPFLAGS@ @LIBMAUSPKGCXXFLAGS@ @LIBMAUSARCHCFLAGS@ -I${includedir}
--- a/libmaus2seqchksumsfactory.pc.in
+++ b/libmaus2seqchksumsfactory.pc.in
-prefix=@prefix@
-exec_prefix=@exec_prefix@
-libdir=@libdir@
-includedir=@includedir@
-
-Name: libmaus2seqchksumsfactory
-Description: non pic digest routines in libmaus2
-Requires: @ZLIBREQ@ @NETTLEREQ@ libmaus2digests
-Version: @VERSION@
-Libs: -L${libdir} -lmaus2seqchksumsfactory @GMPLDFLAGS@ @GMPLIBS@
-Cflags: @LIBMAUSCPPFLAGS@ @LIBMAUSPKGCPPFLAGS@ @LIBMAUSPKGCXXFLAGS@ @LIBMAUSARCHCFLAGS@ @ZLIBCPPFLAGS@ @GMPCPPFLAGS@ -I${includedir}
--- a/src/Makefile.am
+++ b/src/Makefile.am
 ACLOCAL_AMFLAGS=-I m4

 EXTRA_DIST = \
-	libmaus2/digest/sha256_sse4.asm \
-	libmaus2/digest/sha512_sse4.asm \
-	libmaus2/digest/sha256_avx1.asm \
-	libmaus2/digest/sha512_avx.asm \
-	libmaus2/digest/sha256_avx2_rorx2.asm \
-	libmaus2/digest/sha256_avx2_rorx8.asm \
-	libmaus2/digest/sha512_avx2_rorx.asm \
 	libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreTemplate.cpp \
 	libmaus2/lcs/SimdX86BandedGlobalAlignmentTemplate.cpp \
 	libmaus2/lcs/SimdX86GlobalAlignmentTemplate.cpp
@@ -16,7 +9,7 @@ abs_builddir = @abs_builddir@
 abs_srcdir = @abs_srcdir@

 lib_LTLIBRARIES = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la
-lib_LIBRARIES = libmaus2digests.a libmaus2digests_sse4.a libmaus2_irods.a libmaus2seqchksumsfactory.a libmaus2fftw.a
+lib_LIBRARIES = libmaus2_irods.a

 libmaus2_simd_align_128_la_SOURCES = \
 	libmaus2/lcs/SimdX86GlobalAlignmentConstants128.cpp \
@@ -41,42 +34,10 @@ libmaus2_simd_align_256_la_LDFLAGS = @LIBMAUSLDFLAGS@ -version-info ${LIBRARY_VE
 libmaus2_modules_LTLIBRARIES = libmaus2_scram_mod.la
 libmaus2_modulesdir = $(libdir)/libmaus2/$(PACKAGE_VERSION)

-libmaus2digests_a_SOURCES = libmaus2/digest/SHA2_256_sse4.cpp libmaus2/digest/SHA2_512_sse4.cpp libmaus2/digest/DigestFactory_SHA2_ASM.cpp
-libmaus2digests_a_DEPENDENCIES = @DIGESTASMOBJ@
-libmaus2digests_a_LIBADD = @DIGESTASMOBJ@
-libmaus2digests_a_CXXFLAGS = ${AM_CXXFLAGS} @WARNCXXFLAGS@
-
-libmaus2digests_sse4_a_SOURCES = libmaus2/digest/CRC32C_sse42.cpp libmaus2/digest/DigestFactory_CRC32C_SSE42.cpp
-libmaus2digests_sse4_a_CXXFLAGS = ${AM_CXXFLAGS} @WARNCXXFLAGS@ @MSSE4@
-
 libmaus2_irods_a_SOURCES = libmaus2/irods/IRodsSystem.cpp libmaus2/irods/IRodsFileBase.cpp
 libmaus2_irods_a_CPPFLAGS = ${AM_CPPFLAGS} @IRODSCPPFLAGS@
 libmaus2_irods_a_CXXFLAGS = ${AM_CXXFLAGS} @WARNCXXFLAGS@

-libmaus2seqchksumsfactory_a_SOURCES = libmaus2/bambam/ChecksumsFactory.cpp
-libmaus2seqchksumsfactory_a_CPPFLAGS = ${AM_CPPFLAGS} @GMPCPPFLAGS@ @LIBDEFLATECPPFLAGS@
-libmaus2seqchksumsfactory_a_CXXFLAGS = ${AM_CPPFLAGS} @WARNCXXFLAGS@
-
-libmaus2fftw_a_SOURCES = libmaus2/math/binom_fftw.cpp libmaus2/math/Convolution_fftw.cpp
-libmaus2fftw_a_CXXFLAGS = ${AM_CXXFLAGS} @WARNCXXFLAGS@ @FFTWCPPFLAGS@
-
-CLEANFILES=sha256_sse4.o sha256_avx1.o sha256_avx2_rorx2.o sha256_avx2_rorx8.o sha512_avx2_rorx.o sha512_avx.o sha512_sse4.o
-
-sha256_sse4.o: $(abs_srcdir)/libmaus2/digest/sha256_sse4.asm
-	@YASMEXE@ -f x64 -f elf64 -X gnu -g dwarf2 -D LINUX -o sha256_sse4.o $(abs_srcdir)/libmaus2/digest/sha256_sse4.asm
-sha256_avx1.o: $(abs_srcdir)/libmaus2/digest/sha256_avx1.asm
-	@YASMEXE@ -f x64 -f elf64 -X gnu -g dwarf2 -D LINUX -o sha256_avx1.o $(abs_srcdir)/libmaus2/digest/sha256_avx1.asm
-sha256_avx2_rorx2.o: $(abs_srcdir)/libmaus2/digest/sha256_avx2_rorx2.asm
-	@YASMEXE@ -f x64 -f elf64 -X gnu -g dwarf2 -D LINUX -o sha256_avx2_rorx2.o $(abs_srcdir)/libmaus2/digest/sha256_avx2_rorx2.asm
-sha256_avx2_rorx8.o: $(abs_srcdir)/libmaus2/digest/sha256_avx2_rorx8.asm
-	@YASMEXE@ -f x64 -f elf64 -X gnu -g dwarf2 -D LINUX -o sha256_avx2_rorx8.o $(abs_srcdir)/libmaus2/digest/sha256_avx2_rorx8.asm
-sha512_avx2_rorx.o: $(abs_srcdir)/libmaus2/digest/sha512_avx2_rorx.asm
-	@YASMEXE@ -f x64 -f elf64 -X gnu -g dwarf2 -D LINUX -o sha512_avx2_rorx.o $(abs_srcdir)/libmaus2/digest/sha512_avx2_rorx.asm
-sha512_avx.o: $(abs_srcdir)/libmaus2/digest/sha512_avx.asm
-	@YASMEXE@ -f x64 -f elf64 -X gnu -g dwarf2 -D LINUX -o sha512_avx.o $(abs_srcdir)/libmaus2/digest/sha512_avx.asm
-sha512_sse4.o: $(abs_srcdir)/libmaus2/digest/sha512_sse4.asm
-	@YASMEXE@ -f x64 -f elf64 -X gnu -g dwarf2 -D LINUX -o sha512_sse4.o $(abs_srcdir)/libmaus2/digest/sha512_sse4.asm
-
 libmaus2_la_SOURCES = libmaus2/StaticInitialization.cpp \
 	libmaus2/autoarray/AutoArray.cpp \
 	libmaus2/bitio/CompactArray.cpp libmaus2/rank/RankTable.cpp \
@@ -198,14 +159,12 @@ libmaus2_la_SOURCES = libmaus2/StaticInitialization.cpp \
 	libmaus2/lcs/AlignerFactory.cpp \
 	libmaus2/lcs/BandedAlignerFactory.cpp \
 	libmaus2/aio/InputStreamInstance.cpp \
-	libmaus2/lcs/DalignerNP.cpp \
 	libmaus2/aio/OutputStreamInstance.cpp \
 	libmaus2/aio/OutputStreamFactoryContainer.cpp \
 	libmaus2/dazzler/align/TraceBlock.cpp \
 	libmaus2/dazzler/align/ApproximateRun.cpp \
 	libmaus2/suffixsort/BwtMergeBlockSortRequest.cpp \
 	libmaus2/dazzler/align/OverlapMeta.cpp \
-	libmaus2/lcs/DalignerLocalAlignment.cpp \
 	libmaus2/dazzler/align/Tandem.cpp \
 	libmaus2/dazzler/align/TandemVector.cpp \
 	libmaus2/math/GmpInteger.cpp \
@@ -216,6 +175,7 @@ libmaus2_la_SOURCES = libmaus2/StaticInitialization.cpp \
 	libmaus2/fastx/DNAIndexMetaDataSequence.cpp \
 	libmaus2/fastx/DNAIndexMetaData.cpp \
 	libmaus2/bambam/PileVectorElement.cpp \
+	libmaus2/bambam/PileQualityVectorElement.cpp \
 	libmaus2/digest/SHA3_256.cpp \
 	libmaus2/fastx/DNAIndexMetaDataBigBand.cpp \
 	libmaus2/fastx/DNAIndexMetaDataBigBandBiDir.cpp \
@@ -256,14 +216,22 @@ libmaus2_la_SOURCES = libmaus2/StaticInitialization.cpp \
 	libmaus2/aio/PosixFdInput.cpp \
 	libmaus2/parallel/StdSemaphore.cpp \
 	libmaus2/lz/BgzfDeflateHeaderFunctions.cpp \
-	libmaus2/lz/BgzfDeflateZStreamBase.cpp
+	libmaus2/lz/BgzfDeflateZStreamBase.cpp \
+	libmaus2/gtf/CDS.cpp \
+	libmaus2/gtf/Exon.cpp \
+	libmaus2/gtf/ExonInfo.cpp \
+	libmaus2/gtf/ExonInterval.cpp \
+	libmaus2/gtf/ExonSubInfo.cpp \
+	libmaus2/protein/Blosum62.cpp \
+	libmaus2/bambam/ChecksumsFactory.cpp \
+	libmaus2/vcf/VCFSortEntry.cpp

 noinst_HEADERS = libmaus2/lz/lz4.h

-libmaus2_la_CPPFLAGS = ${AM_CPPFLAGS} @LIBMAUSCPPFLAGS@ @SNAPPYCPPFLAGS@ @ZLIBCPPFLAGS@ @GNUTLSCPPFLAGS@ @NETTLECPPFLAGS@ @IGZIPCPPFLAGS@ @DALIGNERCPPFLAGS@ @GMPCPPFLAGS@ @LIBMAUS2_LZMA_CPPFLAGS@ @LIBDEFLATECPPFLAGS@
+libmaus2_la_CPPFLAGS = ${AM_CPPFLAGS} @LIBMAUSCPPFLAGS@ @SNAPPYCPPFLAGS@ @ZLIBCPPFLAGS@ @GNUTLSCPPFLAGS@ @NETTLECPPFLAGS@ @IGZIPCPPFLAGS@ @GMPCPPFLAGS@ @LIBMAUS2_LZMA_CPPFLAGS@ @LIBDEFLATECPPFLAGS@
 libmaus2_la_CXXFLAGS = @LIBMAUSCXXFLAGS@ ${AM_CXXFLAGS} @WARNCXXFLAGS@
-libmaus2_la_LDFLAGS = @LIBMAUSLDFLAGS@ @SNAPPYLDFLAGS@ -version-info ${LIBRARY_VERSION} @LIBMAUSSTATIC@ @IGZIPLDFLAGS@ @GNUTLSLDFLAGS@ @NETTLELDFLAGS@ @DALIGNERLDFLAGS@ @GMPLDFLAGS@ @LIBDEFLATELDFLAGS@
-libmaus2_la_LIBADD = @DLLIB@ @SNAPPYLIBS@ @ZLIBLIBS@ @IGZIPLIBS@ @GNUTLSLIBS@ @NETTLELIBS@ @DALIGNERLIBS@ @GMPLIBS@ @LIBMAUS2_LZMA_LIBS@ @LIBDEFLATELIBS@
+libmaus2_la_LDFLAGS = @LIBMAUSLDFLAGS@ @SNAPPYLDFLAGS@ -version-info ${LIBRARY_VERSION} @LIBMAUSSTATIC@ @IGZIPLDFLAGS@ @GNUTLSLDFLAGS@ @NETTLELDFLAGS@ @GMPLDFLAGS@ @LIBDEFLATELDFLAGS@
+libmaus2_la_LIBADD = @DLLIB@ @SNAPPYLIBS@ @ZLIBLIBS@ @IGZIPLIBS@ @GNUTLSLIBS@ @NETTLELIBS@ @GMPLIBS@ @LIBMAUS2_LZMA_LIBS@ @LIBDEFLATELIBS@

 libmaus2_scram_mod_la_CPPFLAGS = @IOLIBCPPFLAGS@ @LIBMAUSCPPFLAGS@ ${AM_CPPFLAGS} 
 libmaus2_scram_mod_la_CXXFLAGS = @LIBMAUSCXXFLAGS@ ${AM_CXXFLAGS} @WARNCXXFLAGS@ -fPIC
@@ -342,6 +310,30 @@ libmaus2dazzlerstringgraph_include_HEADERS = libmaus2/dazzler/stringgraph/Edge.h
 	libmaus2/dazzler/stringgraph/ContainmentInfo.hpp \
 	libmaus2/dazzler/stringgraph/TraversalElement.hpp

+libmaus2gtf_includedir=$(includedir)/libmaus2/gtf/
+libmaus2gtf_include_HEADERS = \
+	libmaus2/gtf/BAMGTFMap.hpp \
+	libmaus2/gtf/CDS.hpp \
+	libmaus2/gtf/Exon.hpp \
+	libmaus2/gtf/ExonIdOffsetComparator.hpp \
+	libmaus2/gtf/ExonInfo.hpp \
+	libmaus2/gtf/ExonInterval.hpp \
+	libmaus2/gtf/ExonSubInfo.hpp \
+	libmaus2/gtf/Gene.hpp \
+	libmaus2/gtf/GeneChrComparator.hpp \
+	libmaus2/gtf/GeneRangeSets.hpp \
+	libmaus2/gtf/GTFData.hpp \
+	libmaus2/gtf/IntervalList.hpp \
+	libmaus2/gtf/IntervalListSet.hpp \
+	libmaus2/gtf/RangeSets.hpp \
+	libmaus2/gtf/Transcript.hpp \
+	libmaus2/gtf/TranscriptRangeSets.hpp
+
+libmaus2protein_includedir=$(includedir)/libmaus2/protein/
+libmaus2protein_include_HEADERS = \
+	libmaus2/protein/Align.hpp \
+	libmaus2/protein/Blosum62.hpp
+
 libmaus2autoarray_includedir=$(includedir)/libmaus2/autoarray/
 libmaus2autoarray_include_HEADERS = libmaus2/autoarray/AutoArray.hpp libmaus2/autoarray/AutoArray2d.hpp libmaus2/autoarray/AutoArrayMultiMap.hpp \
 	libmaus2/autoarray/GenericAlignedAllocation.hpp
@@ -656,6 +648,7 @@ libmaus2bambam_include_HEADERS = libmaus2/bambam/DecoderBase.hpp libmaus2/bambam
 	libmaus2/bambam/ChecksumsInterfaceTypeInfo.hpp \
 	libmaus2/bambam/StrCmpNumRecode.hpp \
 	libmaus2/bambam/PileVectorElement.hpp \
+	libmaus2/bambam/PileQualityVectorElement.hpp \
 	libmaus2/bambam/CigarStringReader.hpp \
 	libmaus2/bambam/BamAlignmentHashComparator.hpp \
 	libmaus2/bambam/CigarRunLengthDecoder.hpp \
@@ -1173,7 +1166,11 @@ libmaus2math_include_HEADERS=\
 	libmaus2/math/RationalPolynomialSupport.hpp \
 	libmaus2/math/ConstantSumCombinatorics.hpp \
 	libmaus2/math/LGammaCache.hpp \
-	libmaus2/math/Bernoulli.hpp
+	libmaus2/math/Bernoulli.hpp \
+	libmaus2/math/NormalDistribution.hpp \
+	libmaus2/math/LogNormalDistribution.hpp \
+	libmaus2/math/Distribution.hpp \
+	libmaus2/math/HistogramBuckets.hpp

 libmaus2rl_includedir=$(includedir)/libmaus2/rl
 libmaus2rl_include_HEADERS=\
@@ -1185,7 +1182,14 @@ libmaus2posix_include_HEADERS=\

 libmaus2vcf_includedir=$(includedir)/libmaus2/vcf
 libmaus2vcf_include_HEADERS=\
-	libmaus2/vcf/VCFParser.hpp
+	libmaus2/vcf/VCFParser.hpp \
+	libmaus2/vcf/VCFSortEntry.hpp \
+	libmaus2/vcf/VCFSorter.hpp
+
+libmaus2vep_includedir=$(includedir)/libmaus2/vep
+libmaus2vep_include_HEADERS=\
+	libmaus2/vep/VEPCoordinate.hpp \
+	libmaus2/vep/VEPParser.hpp

 libmaus2util_includedir=$(includedir)/libmaus2/util
 libmaus2util_include_HEADERS=\
@@ -1606,19 +1610,12 @@ libmaus2digest_include_HEADERS=\
 	libmaus2/digest/CRC32.hpp \
 	libmaus2/digest/Digests.hpp \
 	libmaus2/digest/Null.hpp \
-	libmaus2/digest/SHA2_256_sse4.hpp \
-	libmaus2/digest/sha256.h \
-	libmaus2/digest/sha512.h \
-	libmaus2/digest/SHA2_512_sse4.hpp \
-	libmaus2/digest/CRC32C_sse42.hpp \
 	libmaus2/digest/CRC32C_Core.hpp \
 	libmaus2/digest/CRC32C.hpp \
 	libmaus2/digest/CRC32_Core.hpp \
 	libmaus2/digest/DigestInterface.hpp \
 	libmaus2/digest/DigestFactory.hpp \
 	libmaus2/digest/DigestFactoryContainer.hpp \
-	libmaus2/digest/DigestFactory_SHA2_ASM.hpp \
-	libmaus2/digest/DigestFactory_CRC32C_SSE42.hpp \
 	libmaus2/digest/DigestFactoryInterface.hpp \
 	libmaus2/digest/md5.hpp \
 	libmaus2/digest/md5.h \
@@ -1888,8 +1885,6 @@ libmaus2lcs_include_HEADERS=\
 	libmaus2/lcs/NNPTraceElement.hpp \
 	libmaus2/lcs/NNPTraceContainer.hpp \
 	libmaus2/lcs/NNPAlignResult.hpp \
-	libmaus2/lcs/DalignerNP.hpp \
-	libmaus2/lcs/DalignerLocalAlignment.hpp \
 	libmaus2/lcs/ScoreBandedAligner.hpp \
 	libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreTemplate.hpp \
 	libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16.hpp \
@@ -2509,10 +2504,10 @@ testunsignedinteger_LDADD = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd
 testunsignedinteger_CXXFLAGS = ${AM_CXXFLAGS} @WARNCXXFLAGS@ 

 testsha_SOURCES = test/testsha.cpp
-testsha_LDADD = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la @NETTLELIBS@ libmaus2digests.a libmaus2digests_sse4.a
+testsha_LDADD = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la @NETTLELIBS@
 testsha_CPPFLAGS = ${AM_CPPFLAGS} @NETTLECPPFLAGS@
 testsha_LDFLAGS = ${AM_LDFLAGS} @NETTLELDFLAGS@
-testsha_DEPENDENCIES = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la libmaus2digests.a libmaus2digests_sse4.a
+testsha_DEPENDENCIES = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la
 testsha_CXXFLAGS = ${AM_CXXFLAGS} @WARNCXXFLAGS@ 

 testmd5_SOURCES = test/testmd5.cpp
@@ -2524,7 +2519,7 @@ testparallelbamrewrite_LDADD = libmaus2.la libmaus2_simd_align_128.la libmaus2_s
 testparallelbamrewrite_CXXFLAGS = ${AM_CXXFLAGS} @WARNCXXFLAGS@ 

 testparallelbamblocksort_SOURCES = test/testparallelbamblocksort.cpp
-testparallelbamblocksort_LDADD = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la @SNAPPYLIBS@ ${DLLIB} libmaus2seqchksumsfactory.a libmaus2digests.a libmaus2digests_sse4.a @GMPLIBS@
+testparallelbamblocksort_LDADD = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la @SNAPPYLIBS@ ${DLLIB} @GMPLIBS@
 testparallelbamblocksort_CPPFLAGS = ${AM_CPPFLAGS} ${CPPFLAGS} @SNAPPYCPPFLAGS@
 testparallelbamblocksort_CXXFLAGS = ${AM_CXXFLAGS} @WARNCXXFLAGS@
 testparallelbamblocksort_LDFLAGS = ${AM_LDFLAGS} ${LDFLAGS} @SNAPPYLDFLAGS@ @GMPLDFLAGS@
@@ -2555,10 +2550,10 @@ testsamrecoding_LDADD    = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_
 testsamrecoding_CXXFLAGS = ${AM_CXXFLAGS} @WARNCXXFLAGS@

 testdazzlerdb_SOURCES  = test/testdazzlerdb.cpp
-testdazzlerdb_LDADD    = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la ${DLLIB} @DALIGNERLIBS@
-testdazzlerdb_CPPFLAGS = ${AM_CPPFLAGS} @DALIGNERCPPFLAGS@
+testdazzlerdb_LDADD    = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la ${DLLIB}
+testdazzlerdb_CPPFLAGS = ${AM_CPPFLAGS}
 testdazzlerdb_CXXFLAGS = ${AM_CXXFLAGS} @WARNCXXFLAGS@ 
-testdazzlerdb_LDFLAGS  = ${AM_LDFLAGS} @DALIGNERLDFLAGS@
+testdazzlerdb_LDFLAGS  = ${AM_LDFLAGS}

 testnd_SOURCES  = test/testnd.cpp
 testnd_LDADD    = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la ${DLLIB}
@@ -2701,10 +2696,10 @@ testmatrix_CXXFLAGS = @WARNCXXFLAGS@ ${AM_CXXFLAGS}
 testmatrix_LDFLAGS  = ${AM_LDFLAGS}

 testconvpowercache_SOURCES  = test/testconvpowercache.cpp
-testconvpowercache_LDADD    = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la libmaus2fftw.a ${DLLIB} @FFTWLIBS@
-testconvpowercache_CPPFLAGS = ${AM_CPPFLAGS} @FFTWCPPFLAGS@
+testconvpowercache_LDADD    = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la ${DLLIB}
+testconvpowercache_CPPFLAGS = ${AM_CPPFLAGS}
 testconvpowercache_CXXFLAGS = @WARNCXXFLAGS@ ${AM_CXXFLAGS}
-testconvpowercache_LDFLAGS  = ${AM_LDFLAGS} @FFTWLDFLAGS@
+testconvpowercache_LDFLAGS  = ${AM_LDFLAGS}

 testlassort_SOURCES  = test/testlassort.cpp
 testlassort_LDADD    = libmaus2.la libmaus2_simd_align_128.la libmaus2_simd_align_256.la ${DLLIB}

--- a/src/Makefile.in
+++ b/src/Makefile.in