Loading AUTHORS +0 −1 Original line number Diff line number Diff line Loading @@ -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) ChangeLog +159 −0 Original line number Diff line number Diff line 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 Loading Makefile.am +1 −1 Original line number Diff line number Diff line Loading @@ -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 Loading Makefile.in +57 −101 Original line number Diff line number Diff line Loading @@ -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@) Loading Loading @@ -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 \ Loading Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading Loading @@ -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@ Loading Loading @@ -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 Loading Loading @@ -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 Loading autom4te.cache/output.0 +4599 −6588 File changed.Preview size limit exceeded, changes collapsed. Show changes Loading
AUTHORS +0 −1 Original line number Diff line number Diff line Loading @@ -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)
ChangeLog +159 −0 Original line number Diff line number Diff line 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 Loading
Makefile.am +1 −1 Original line number Diff line number Diff line Loading @@ -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 Loading
Makefile.in +57 −101 Original line number Diff line number Diff line Loading @@ -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@) Loading Loading @@ -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 \ Loading Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading @@ -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@ Loading Loading @@ -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@ Loading Loading @@ -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 Loading Loading @@ -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 Loading
autom4te.cache/output.0 +4599 −6588 File changed.Preview size limit exceeded, changes collapsed. Show changes
