Commit 59a4b494 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.0.653

parent d1c3da1d

.gitignore

+1 −3
Original line number Diff line number Diff line
@@ -70,7 +70,5 @@ test/*.trs 
compile_os_x.sh

bumprun.sh

doconfigclang.sh

<<<<<<< HEAD

removespace.sh

=======

>>>>>>> experimental
 
numproc.sh

AUTHORS

+0 −7
Original line number Diff line number Diff line 
Eva Hash code in src/libmaus2/hashing/hash.hpp by Bob Jenkins, public domain

Oracle LCP code in src/libmaus2/lcp/OracleLCP* by Simon Puglisi, published under GPLv2

Succinct RMQ code in src/libmaus2/rmq/FischerSystematicSuccinctRMQ* by Johannes Fischer, published under GPLv2

NearestNeighbourDictionary code in src/libmaus2/bp/NearestNeighourDictionary.hpp by Simon Gog from the SDSL library, published under GPLv3

Pioneer bitmap code in src/libmaus2/bp/BalancedParenthesesBase.hpp by Simon Gog from SDSL library, published under GPLv3

popcount code in src/libmaus2/rank/popcnt.hpp imported from http://graphics.stanford.edu/~seander/bithacks.html#CountBitsSetParallel, public domain code by Sean Eron Anderson

radixsort code in src/libmaus2/sorting/SerialRadixSort64.hpp adapted from code by Andrew I. Schein (see file for license)

divsufsort code in src/libmaus2/suffixsort/divsufsort* by Yuta Mori (see file for license)

SAIS code in src/libmaus2/suffixsort/SAIS_Mori.hpp by Yuta Mori (see file for license)

md5 code in src/libmaus2/digest/md5.[ch] by L. Peter Deutsch (Aladdin Enterprises) (see file for license)

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)

Part of CRC32{|C} code in src/libmaus2/digest/CRC32{|C}_Core.cpp by Cisco Systems, Inc. and Herbert Xu (GPLv2)

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

+354 −0
Original line number Diff line number Diff line 
libmaus2 (2.0.653-1) unstable; urgency=medium



  * add getNextReferenceLength/getNextFrontDel/getNextReferenceInterval in BamAlignmentDecoderBase/BamAlignment



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 07 Aug 2019 09:01:59 +0200



libmaus2 (2.0.652-1) unstable; urgency=medium



  * fixing reading pos and nextpos from files via io_lib



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 31 Jul 2019 10:33:55 +0200



libmaus2 (2.0.651-1) unstable; urgency=medium



  * extend levelToString to libdeflate settings in BamBlockWriterBaseFactory

  * add DeflateDefaults class for factoring out default deflate compression level

  * add getDefaultLevel in BamBlockWriterBaseFactory



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 30 Jul 2019 17:23:57 +0200



libmaus2 (2.0.650-1) unstable; urgency=medium



  * make writeBlock return number of bytes written in BgzfInflateBase

  * make writeHeader method return number of bytes written in BgzfInflateHeaderBase

  * add concat and getReader methods in TempFileArray



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 26 Jul 2019 16:49:45 +0200



libmaus2 (2.0.649-1) unstable; urgency=medium



  * add shiftValues function in BamNumericalIndexGenerator

  * add replaceValue method in BamNumericalIndexGenerator

  * make throwing exception on eof optional in BamRawDecoder



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 25 Jul 2019 15:08:29 +0200



libmaus2 (2.0.648-1) unstable; urgency=medium



  * remove deprecated CollatingBamDecoder class



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 25 Jul 2019 10:52:40 +0200



libmaus2 (2.0.647-1) unstable; urgency=medium



  * re-add erroneously removed writeBamIndex function in BlockMergeControl



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 24 Jul 2019 14:18:44 +0200



libmaus2 (2.0.646-1) unstable; urgency=medium



  * add numerical indexing in parallel bam sorting

  * automatically disable deepbind if asan is requested in configure

  * store file name provided at construction time in BamNumericalIndexGenerator



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 24 Jul 2019 13:53:05 +0200



libmaus2 (2.0.645-1) unstable; urgency=medium



  * add getContigNames method in VCFParser

  * avoid flush in Histogram printing



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 24 Jul 2019 10:48:06 +0200



libmaus2 (2.0.644-1) unstable; urgency=medium



  * add getType function/method in BamAlignmentDecoderBase/BamAlignment

  * mark getSortOrder as const in BamHeader



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 23 Jul 2019 17:17:02 +0200



libmaus2 (2.0.643-1) unstable; urgency=medium



  * fix tlen field in SCRAM input



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 19 Jul 2019 14:40:19 +0200



libmaus2 (2.0.642-1) unstable; urgency=medium



  * add writeBlock method in BgzfInflateBase

  * add writeHeader method in BgzfInflateHeaderBase

  * use fixed sequence EOF block in BgzfInflateDeflateParallel and BgzfRecode instead of producing one using zlib

  * add toString method in BgzfInflateInfo

  * be more verbose about unexpected EOF in BgzfInflateBase

  * use fixed sequence EOF block in BgzfDeflate instead of producing one via zlib

  * add getEOFBlock function in BgzfDeflateBase

  * add getHeader method in BamRawDecoder

  * add flush call in BamNumExtractor



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 19 Jul 2019 11:08:10 +0200



libmaus2 (2.0.641-1) unstable; urgency=medium



  * remove RAZF as it is no longer supported by samtools

  * update compression level checking in BamBlockWriterBaseFactory

  * implement libdeflate support for compression



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 18 Jul 2019 10:35:06 +0200



libmaus2 (2.0.640-1) unstable; urgency=medium



  * add unparsedCopy copy method in VCFParser

  * add BgzfDeflateOutputCallbackBamNumericalIndex



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 17 Jul 2019 16:04:24 +0200



libmaus2 (2.0.639-1) unstable; urgency=medium



  * replace stdc++ by stdcxx in aio factory containers

  * improve exception handling in StdThread

  * fix return value in BgzfInflateBlock for case of empty blocks inside file



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 16 Jul 2019 13:42:33 +0200



libmaus2 (2.0.638-1) unstable; urgency=medium



  * add readFileAsStream/readStream in GetFileSize

  * add tryoq flag in BAM Checksums



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 16 Jul 2019 10:53:42 +0200



libmaus2 (2.0.637-1) unstable; urgency=medium



  * add extract variant for BamNumExtractor



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 12 Jul 2019 15:08:06 +0200



libmaus2 (2.0.636-1) unstable; urgency=medium



  * add BamNumExtractor

  * add getRawDecoderAt method in BamNumericalIndexDecoder

  * add BamRawDecoder test

  * add BamRawDecoder class



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Mon, 08 Jul 2019 12:26:20 +0200



libmaus2 (2.0.635-1) unstable; urgency=medium



  * add posix_WIFEXTED and posix_WEXITSTATUS in PosixFunctions

  * rename function lseek in PosixFunctions to posix_lseek to avoid clashing with a macro definition of lseek

  * add EXEEXT ending for optionally built programs in configure



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 05 Jul 2019 09:01:35 +0200



libmaus2 (2.0.634-1) unstable; urgency=medium

 

  * remove HDF5 wrapper

  * remove libarchive test program

  * remove dead/unused code

  * refactor LibMausException (move code to .cpp file)

  * add some locking typedefs

  * remove posix regex interface

  * replace PosixThread class by StdThread and remove PosixThread/PosixMutex/PosixSpinLock

  * replace PosixMutex by StdMutex

  * replace PosixSpinLock by StdSpinLock

  * cleanup/move to Std instead of Posix

  * remove outdated ThreadPool framework

  * replace Posix by Std

  * rewrite some data structures to use std:: instead of Posix functionality

  * remove TerminatableSynchronousHeap and replace by StdTerminatableSynchronousHeap

  * replace TerminatableSynchronousHeap by StdTerminatableSynchronousHeap in SimpleThreadPool

  * add StdTerminatableSynchronousHeap

  * add unlock/lock in ScopeStdMutex

  * add StdSemaphore

  * add StdMutex and StdSpinLock

  * fix warnings in bitbtree

  * add StdThread class

  * split PosixFdInput into hpp/cpp

  * return not supported error code instead of throwing exception in PosixFunctions::getFIOsizeViaFStatFS

  * namespace cleanup (move most posix calls in aio to PosixFunctions class)



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 03 Jul 2019 20:26:18 +0200



libmaus2 (2.0.633-1) unstable; urgency=medium



  * start to move posix calls into a separate interface

  * add automatic decompression of gzipped input in VCFParser

  * add runPatchContigPrepend function in VCFParser



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 28 Jun 2019 13:39:02 +0200



libmaus2 (2.0.632-1) unstable; urgency=medium



  * add TabEntry and VCFParser classes

  * add detection of libdeflate in configure.ac



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 27 Jun 2019 20:25:09 +0200



libmaus2 (2.0.631-1) unstable; urgency=medium



  * do not leave behind unused temp files in BlockSortControl



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 19 Jun 2019 10:45:40 +0200



libmaus2 (2.0.630-1) unstable; urgency=medium



  * add copyFrom method in FiniteSizeHeap



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 18 Jun 2019 17:48:45 +0200



libmaus2 (2.0.629-1) unstable; urgency=medium



  * add missing const marker for top method in FiniteSizeHeap



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 18 Jun 2019 16:51:44 +0200



libmaus2 (2.0.628-1) unstable; urgency=medium



  * fix compilation error due to missing OFStreamOutputStreamFactory::copy

  * rename/introduce stdc++ stream in aio factories



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 18 Jun 2019 15:51:25 +0200



libmaus2 (2.0.627-1) unstable; urgency=medium



  * add pointer type in ScopePosixMutex

  * add bundle script

  * extend mapBA in PosMapping

  * add PosMapping class

  * remove SocketPair class



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 18 Jun 2019 13:49:20 +0200



libmaus2 (2.0.626-1) unstable; urgency=medium



  * code cleanup



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 14 Jun 2019 15:08:32 +0200



libmaus2 (2.0.625-1) unstable; urgency=medium



  * code cleanup

  * remove reference to GenericInput class in testHuffman

  * replace direct posix calls in LineSplittingPosixFdOutputStreamBuffer by OutputStreamInstance

  * remove references to Posix from FastWriteBitWriter.hpp and MarkerFastWriteBitWriter.hpp

  * remove direct calls to (Input|Output)StreamFactory*::construct* where possible



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 14 Jun 2019 10:46:32 +0200



libmaus2 (2.0.624-1) unstable; urgency=medium



  * add replaceCigar function in BamAlignmentEncoderBase



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 13 Jun 2019 12:55:57 +0200



libmaus2 (2.0.623-1) unstable; urgency=medium



  * add replaceSequence in BamAlignmentEncoderBase

  * add getNumPreQualBytes/getNumQualBytes/getNumPostQualBytes/getNumPostSeqBytes in BamAlignmentDecoderBase



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 13 Jun 2019 10:07:02 +0200



libmaus2 (2.0.622-1) unstable; urgency=medium



  * allow setting of error stream in BamAlignmentDecoderBase::calmd

  * add pointer types in MdStringComputationContext



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 12 Jun 2019 16:35:44 +0200



libmaus2 (2.0.621-1) unstable; urgency=medium



  * add replaceName function in BamAlignmentDecoderBase



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 12 Jun 2019 10:32:49 +0200



libmaus2 (2.0.620-1) unstable; urgency=medium



  * add shared pointer type in BamAuxFilterVector



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 12 Jun 2019 08:33:12 +0200



libmaus2 (2.0.619-1) unstable; urgency=medium



  * fix order in SimpleThreadWorkPackageComparator

  * print package name in SimpleThreadWorkPackage output operator

  * add printPending method in SimpleThreadPool



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 11 Jun 2019 14:47:05 +0200



libmaus2 (2.0.618-1) unstable; urgency=medium



  * remove custom popcount c++ code and replace by calling std::bitset<>::count

  * remove unused files

  * general cleanup

  * remove SAIS part from AUTHORS list after removing SAIS code



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 07 Jun 2019 12:50:59 +0200



libmaus2 (2.0.617-1) unstable; urgency=medium



  * remove OS and SAIS code

  * remove code imported from Linux kernel in CRC32_Core.cpp/CRC32C_Core.cpp by putting preprocessor statements modifying x86_64 code as needed for general case

  * remove Fischer systematic succinct RMQ code

  * remove nearest neighbour dictionary code

  * remove balanced parantheses code

  * remove oracle LCP code reference in AUTHORS

  * remove OracleLCP code



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 06 Jun 2019 14:08:24 +0200



libmaus2 (2.0.616-1) unstable; urgency=medium



  * be more verbose in GzipHeaderParser error messages

  * add reset method in GzipHeaderParser



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 06 Jun 2019 12:24:30 +0200



libmaus2 (2.0.615-1) unstable; urgency=medium



  * no change version bump to check version bumping script



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 05 Jun 2019 17:19:57 +0200



libmaus2 (2.0.612-1) unstable; urgency=medium



  * update information in bumpversion script

  * remove non source files from branch

  * install CheckSelf.hpp

  * install LibMausWindows.hpp

  * add putFastQCasava18 in BamAlignmentDecoderBase

  * fix warnings about limited range of data type in SamInfo

  * add BamAlignmentNameLexicographicComparator

  * allow error bound in NPLLinMem

  * use CheckSelf in NP to allow for different iterator type for a and b string in npTemplate

  * add valid flag for return value of NPLNoTrace to allow for limited error number calls

  * directly call template function in NPLinMem to avoid instantiation of eq comparison for different iterator types

  * allow different iterator type for a and b string in NPNoTrace

  * add CheckSelf template class in lcs

  * fail in DatabaseFile::writeDatabase if symlink syscall is not available

  * do not directly include windows.h in AutoArray

  * check for presence of fsync in SynchronousGenericOutputPosix (otherwise do not flush...)

  * conditional compilation of mkdir based on number of parameters used in PosixFdOutputStreamFactory

  * check for presence of fsync in PosixFdOutputStreamBuffer (otherwise do not flush...)

  * check for fsync presence in PosixFdInputOutputStreamBuffer (otherwise do not flush...)

  * check for presence of O_LARGEFILE in PosixFdInput

  * add string/filename based constructor in FastALineParser

  * add byteSize method in NPL class

  * use different pagesize function

  * fix missing parameter in ImpHuffmanWaveletLF constructor

  * add various compilation options in Socket based on presence/absence of headers/system calls

  * fail in sendReceiveFd if system calls are not available

  * fail in Command if fork system call is not available

  * fail in LogPipe if fork or pipe system call are not available

  * add missing include directives in LogPipe.hpp

  * fail in LogPipeMultiplex if fork or pipe system call not available

  * add missing include directives in LogPipeMultiplex

  * fail in LogPipeMultiplexGeneric if fork or pipe system call not available

  * add missing include directives in LogPipeMultiplexGeneric

  * fail in PosixExecute if fork or pipe system call are not available

  * check for presence of SIG_HUP and SIG_PIPE in TempFileRemovalContainer

  * check for presence of ioctl in Terminal

  * add more checks in configure



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 29 May 2019 14:00:08 +0200



libmaus2 (2.0.611-1) unstable; urgency=medium



  * add verbose mode in copyToPrefix for DatabaseFile

INSTALL

+161 −159

File changed.

Preview size limit exceeded, changes collapsed.

Makefile.in

+69 −19
Original line number Diff line number Diff line 
# Makefile.in generated by automake 1.15.1 from Makefile.am.

# Makefile.in generated by automake 1.15 from Makefile.am.

# @configure_input@



# Copyright (C) 1994-2017 Free Software Foundation, Inc.

# Copyright (C) 1994-2014 Free Software Foundation, Inc.



# This Makefile.in is free software; the Free Software Foundation

# gives unlimited permission to copy and/or distribute it,
@@ -281,6 +281,7 @@ ECHO_T = @ECHO_T@ 
EGREP = @EGREP@

ENDIANESS = @ENDIANESS@

EXEEXT = @EXEEXT@

FCNTL_H = @FCNTL_H@

FFTWCPPFLAGS = @FFTWCPPFLAGS@

FFTWLDFLAGS = @FFTWLDFLAGS@

FFTWLIBS = @FFTWLIBS@
@@ -295,7 +296,7 @@ GNUTLSLDFLAGS = @GNUTLSLDFLAGS@ 
GNUTLSLIBS = @GNUTLSLIBS@

GNUTLSREQ = @GNUTLSREQ@

GREP = @GREP@

HAVEAIO = @HAVEAIO@

HAVEARPAINETH = @HAVEARPAINETH@

HAVEBACKTRACE = @HAVEBACKTRACE@

HAVEDARWINSPINLOCKS = @HAVEDARWINSPINLOCKS@

HAVEDLFCNH = @HAVEDLFCNH@
@@ -304,6 +305,10 @@ HAVEHAVEFEATURESH = @HAVEHAVEFEATURESH@ 
HAVEI386 = @HAVEI386@

HAVELINUXSYSCTLH = @HAVELINUXSYSCTLH@

HAVEMSGCMSGCLOEXEC = @HAVEMSGCMSGCLOEXEC@

HAVENETDBH = @HAVENETDBH@

HAVENETINETINH = @HAVENETINETINH@

HAVENETINETTCPH = @HAVENETINETTCPH@

HAVEPOLLH = @HAVEPOLLH@

HAVEPOSIXMEMALIGN = @HAVEPOSIXMEMALIGN@

HAVEPRCTL = @HAVEPRCTL@

HAVEPTHREADATTRSETAFFINITYNP = @HAVEPTHREADATTRSETAFFINITYNP@
@@ -319,22 +324,21 @@ 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@

HDF5CPPFLAGS = @HDF5CPPFLAGS@

HDF5CXXFLAGS = @HDF5CXXFLAGS@

HDF5DIR = @HDF5DIR@

HDF5LDFLAGS = @HDF5LDFLAGS@

HDF5LIBS = @HDF5LIBS@

IGZIPCPPFLAGS = @IGZIPCPPFLAGS@

IGZIPLDFLAGS = @IGZIPLDFLAGS@

IGZIPLIBS = @IGZIPLIBS@
@@ -358,45 +362,91 @@ IRODSLDFLAGS = @IRODSLDFLAGS@ 
IRODSLIBS = @IRODSLIBS@

LD = @LD@

LDFLAGS = @LDFLAGS@

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_FILEOFFSET_BITS = @LIBMAUS2_FILEOFFSET_BITS@

LIBMAUS2_HAVE_ALIGNMENT_ONE_TO_MANY_AVX2 = @LIBMAUS2_HAVE_ALIGNMENT_ONE_TO_MANY_AVX2@

LIBMAUS2_HAVE_AVX = @LIBMAUS2_HAVE_AVX@

LIBMAUS2_HAVE_AVX2 = @LIBMAUS2_HAVE_AVX2@

LIBMAUS2_HAVE_BASENAME = @LIBMAUS2_HAVE_BASENAME@

LIBMAUS2_HAVE_CLOSE = @LIBMAUS2_HAVE_CLOSE@

LIBMAUS2_HAVE_DALIGNER = @LIBMAUS2_HAVE_DALIGNER@

LIBMAUS2_HAVE_DIRNAME = @LIBMAUS2_HAVE_DIRNAME@

LIBMAUS2_HAVE_EXECINFO_H = @LIBMAUS2_HAVE_EXECINFO_H@

LIBMAUS2_HAVE_FCNTL = @LIBMAUS2_HAVE_FCNTL@

LIBMAUS2_HAVE_FFTW = @LIBMAUS2_HAVE_FFTW@

LIBMAUS2_HAVE_FORK = @LIBMAUS2_HAVE_FORK@

LIBMAUS2_HAVE_FSTAT = @LIBMAUS2_HAVE_FSTAT@

LIBMAUS2_HAVE_FSTATFS = @LIBMAUS2_HAVE_FSTATFS@

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_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_HDF5 = @LIBMAUS2_HAVE_HDF5@

LIBMAUS2_HAVE_HSTRERROR = @LIBMAUS2_HAVE_HSTRERROR@

LIBMAUS2_HAVE_IGZIP = @LIBMAUS2_HAVE_IGZIP@

LIBMAUS2_HAVE_IRODS = @LIBMAUS2_HAVE_IRODS@

LIBMAUS2_HAVE_LIBARCHIVE = @LIBMAUS2_HAVE_LIBARCHIVE@

LIBMAUS2_HAVE_LSEEK = @LIBMAUS2_HAVE_LSEEK@

LIBMAUS2_HAVE_LZMA = @LIBMAUS2_HAVE_LZMA@

LIBMAUS2_HAVE_MMAP = @LIBMAUS2_HAVE_MMAP@

LIBMAUS2_HAVE_MMAP_HUGEPAGES = @LIBMAUS2_HAVE_MMAP_HUGEPAGES@

LIBMAUS2_HAVE_OFF_T = @LIBMAUS2_HAVE_OFF_T@

LIBMAUS2_HAVE_OPEN_2 = @LIBMAUS2_HAVE_OPEN_2@

LIBMAUS2_HAVE_OPEN_3 = @LIBMAUS2_HAVE_OPEN_3@

LIBMAUS2_HAVE_O_CREAT = @LIBMAUS2_HAVE_O_CREAT@

LIBMAUS2_HAVE_O_LARGEFILE = @LIBMAUS2_HAVE_O_LARGEFILE@

LIBMAUS2_HAVE_O_NONBLOCK = @LIBMAUS2_HAVE_O_NONBLOCK@

LIBMAUS2_HAVE_O_RDONLY = @LIBMAUS2_HAVE_O_RDONLY@

LIBMAUS2_HAVE_O_RDWR = @LIBMAUS2_HAVE_O_RDWR@

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_READ = @LIBMAUS2_HAVE_READ@

LIBMAUS2_HAVE_SHA2_ASSEMBLY = @LIBMAUS2_HAVE_SHA2_ASSEMBLY@

LIBMAUS2_HAVE_SIGHUP = @LIBMAUS2_HAVE_SIGHUP@

LIBMAUS2_HAVE_SIGPIPE = @LIBMAUS2_HAVE_SIGPIPE@

LIBMAUS2_HAVE_SOCKLEN_T = @LIBMAUS2_HAVE_SOCKLEN_T@

LIBMAUS2_HAVE_SSIZE_T = @LIBMAUS2_HAVE_SSIZE_T@

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_SYMLINK = @LIBMAUS2_HAVE_SYMLINK@

LIBMAUS2_HAVE_SYSCONF = @LIBMAUS2_HAVE_SYSCONF@

LIBMAUS2_HAVE_SYS_SELECT_H = @LIBMAUS2_HAVE_SYS_SELECT_H@

LIBMAUS2_HAVE_SYS_WAIT_H = @LIBMAUS2_HAVE_SYS_WAIT_H@

LIBMAUS2_HAVE_VFS_H = @LIBMAUS2_HAVE_VFS_H@

LIBMAUS2_HAVE_WAITPID = @LIBMAUS2_HAVE_WAITPID@

LIBMAUS2_HAVE_WEXITSTATUS = @LIBMAUS2_HAVE_WEXITSTATUS@

LIBMAUS2_HAVE_WIFEXITED = @LIBMAUS2_HAVE_WIFEXITED@

LIBMAUS2_HAVE_WINSOCK2_H = @LIBMAUS2_HAVE_WINSOCK2_H@

LIBMAUS2_HAVE_WRITE = @LIBMAUS2_HAVE_WRITE@

LIBMAUS2_HAVE_WS2TCPIP_H = @LIBMAUS2_HAVE_WS2TCPIP_H@

LIBMAUS2_IRODS_NEED_PREFIX = @LIBMAUS2_IRODS_NEED_PREFIX@

LIBMAUS2_LARGEFILE_SOURCE = @LIBMAUS2_LARGEFILE_SOURCE@

LIBMAUS2_LIBARCHIVE_CPPFLAGS = @LIBMAUS2_LIBARCHIVE_CPPFLAGS@

LIBMAUS2_LIBARCHIVE_LIBS = @LIBMAUS2_LIBARCHIVE_LIBS@

LIBMAUS2_LIBARCHIVE_REQ = @LIBMAUS2_LIBARCHIVE_REQ@

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@

LIBMAUSARCHCFLAGS = @LIBMAUSARCHCFLAGS@

LIBMAUSCPPFLAGS = @LIBMAUSCPPFLAGS@

LIBMAUSCXXFLAGS = @LIBMAUSCXXFLAGS@

LIBMAUSHAVELIBDEFLATE = @LIBMAUSHAVELIBDEFLATE@

LIBMAUSHAVESNAPPY = @LIBMAUSHAVESNAPPY@

LIBMAUSIRODSPC = @LIBMAUSIRODSPC@

LIBMAUSLDFLAGS = @LIBMAUSLDFLAGS@
@@ -461,7 +511,9 @@ 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@
@@ -514,8 +566,6 @@ htmldir = @htmldir@ 
includedir = @includedir@

infodir = @infodir@

install_sh = @install_sh@

libarchive_CFLAGS = @libarchive_CFLAGS@

libarchive_LIBS = @libarchive_LIBS@

libdir = @libdir@

libexecdir = @libexecdir@

liblzma_CFLAGS = @liblzma_CFLAGS@
@@ -841,7 +891,7 @@ distdir: $(DISTFILES) 
	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \

	|| chmod -R a+r "$(distdir)"

dist-gzip: distdir

	tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz

	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz

	$(am__post_remove_distdir)



dist-bzip2: distdir
@@ -867,7 +917,7 @@ dist-shar: distdir 
	@echo WARNING: "Support for shar distribution archives is" \

	               "deprecated." >&2

	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2

	shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz

	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz

	$(am__post_remove_distdir)



dist-zip: distdir
@@ -885,7 +935,7 @@ dist dist-all: 
distcheck: dist

	case '$(DIST_ARCHIVES)' in \

	*.tar.gz*) \

	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\

	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\

	*.tar.bz2*) \

	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\

	*.tar.lz*) \
@@ -895,7 +945,7 @@ distcheck: dist 
	*.tar.Z*) \

	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\

	*.shar.gz*) \

	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\

	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\

	*.zip*) \

	  unzip $(distdir).zip ;;\

	esac