.gitignore

@@ -70,7 +70,5 @@ test/*.trs
 compile_os_x.sh
 bumprun.sh
 doconfigclang.sh
-<<<<<<< HEAD
 removespace.sh
-=======
->>>>>>> experimental
+numproc.sh

AUTHORS

 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

+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

Makefile.in

-# 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

README.md

@@ -53,10 +53,10 @@ A full list of configuration parameters can be obtained by calling
 
 libmaus2 can use functionality from several other code bases. This includes:
 
- - snappy [http://google.github.io/snappy/] : a fast and lightweight Lempel-Ziv
+ - snappy [https://github.com/google/snappy] : a fast and lightweight Lempel-Ziv
    type compression/decompression library. This can be used for the compression
    of temporary files (as used in name collating BAM input for instance).
- - io_lib [http://sourceforge.net/p/staden/code/HEAD/tree/io_lib/] : This is
+ - io_lib [https://github.com/jkbonfield/io_lib] : This is
    part of the Staden package. libmaus2 can use this library for SAM and CRAM
    file input. The minimum version of io_lib required is 1.14.11.
 

aclocal.m4

-# generated automatically by aclocal 1.15.1 -*- Autoconf -*-
+# generated automatically by aclocal 1.15 -*- Autoconf -*-
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
 
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -296,7 +296,7 @@ AS_VAR_COPY([$1], [pkg_cv_][$1])
 AS_VAR_IF([$1], [""], [$5], [$4])dnl
 ])dnl PKG_CHECK_VAR
 
-# Copyright (C) 2002-2017 Free Software Foundation, Inc.
+# Copyright (C) 2002-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -311,7 +311,7 @@ AC_DEFUN([AM_AUTOMAKE_VERSION],
 [am__api_version='1.15'
 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
 dnl require some minimum version.  Point them to the right macro.
-m4_if([$1], [1.15.1], [],
+m4_if([$1], [1.15], [],
       [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
 ])
 
@@ -327,14 +327,14 @@ m4_define([_AM_AUTOCONF_VERSION], [])
 # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
 # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.15.1])dnl
+[AM_AUTOMAKE_VERSION([1.15])dnl
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
 
 # AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -386,7 +386,7 @@ am_aux_dir=`cd "$ac_aux_dir" && pwd`
 
 # AM_CONDITIONAL                                            -*- Autoconf -*-
 
-# Copyright (C) 1997-2017 Free Software Foundation, Inc.
+# Copyright (C) 1997-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -417,7 +417,7 @@ AC_CONFIG_COMMANDS_PRE(
 Usually this means the macro was only invoked conditionally.]])
 fi])])
 
-# Copyright (C) 1999-2017 Free Software Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -608,7 +608,7 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl
 
 # Generate code to set up dependency tracking.              -*- Autoconf -*-
 
-# Copyright (C) 1999-2017 Free Software Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -684,7 +684,7 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
 
 # Do all the work for Automake.                             -*- Autoconf -*-
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -881,7 +881,7 @@ for _am_header in $config_headers :; do
 done
 echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -902,7 +902,7 @@ if test x"${install_sh+set}" != xset; then
 fi
 AC_SUBST([install_sh])])
 
-# Copyright (C) 2003-2017 Free Software Foundation, Inc.
+# Copyright (C) 2003-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -923,7 +923,7 @@ AC_SUBST([am__leading_dot])])
 
 # Check to see how 'make' treats includes.	            -*- Autoconf -*-
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -973,7 +973,7 @@ rm -f confinc confmf
 
 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
 
-# Copyright (C) 1997-2017 Free Software Foundation, Inc.
+# Copyright (C) 1997-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1014,7 +1014,7 @@ fi
 # Obsolete and "removed" macros, that must however still report explicit
 # error messages when used, to smooth transition.
 #
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1041,7 +1041,7 @@ AU_DEFUN([fp_C_PROTOTYPES], [AM_C_PROTOTYPES])
 
 # Helper functions for option handling.                     -*- Autoconf -*-
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1070,7 +1070,7 @@ AC_DEFUN([_AM_SET_OPTIONS],
 AC_DEFUN([_AM_IF_OPTION],
 [m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
 
-# Copyright (C) 1999-2017 Free Software Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1117,7 +1117,7 @@ AC_LANG_POP([C])])
 # For backward compatibility.
 AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1136,7 +1136,7 @@ AC_DEFUN([AM_RUN_LOG],
 
 # Check to make sure that the build environment is sane.    -*- Autoconf -*-
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1217,7 +1217,7 @@ AC_CONFIG_COMMANDS_PRE(
 rm -f conftest.file
 ])
 
-# Copyright (C) 2009-2017 Free Software Foundation, Inc.
+# Copyright (C) 2009-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1277,7 +1277,7 @@ AC_SUBST([AM_BACKSLASH])dnl
 _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
 ])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1305,7 +1305,7 @@ fi
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 AC_SUBST([INSTALL_STRIP_PROGRAM])])
 
-# Copyright (C) 2006-2017 Free Software Foundation, Inc.
+# Copyright (C) 2006-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1324,7 +1324,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
 
 # Check how to create a tarball.                            -*- Autoconf -*-
 
-# Copyright (C) 2004-2017 Free Software Foundation, Inc.
+# Copyright (C) 2004-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,

bundle.sh

+#!/bin/bash
+D=`date "+%Y_%m_%d"`
+P=`head -n 1 configure.ac | sed "s|AC_INIT(||;s|,.*||"`
+set -x
+git bundle create ../${P}_${D}.bundle --branches --tags