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ChangeLog
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libmaus (0.0.196-1) unstable; urgency=low
* set dup flag instead of just adding it
-- German Tischler <[email protected]> Wed, 25 Mar 2015 14:20:57 +0000
libmaus (0.0.195-1) unstable; urgency=low
* add include statements for off_t on Debian Etch
-- German Tischler <[email protected]> Fri, 13 Feb 2015 10:21:06 +0000
libmaus (0.0.194-1) unstable; urgency=low
* disable stack trace translation in ConstantStringHash when we cannot find a perfect hash
-- German Tischler <[email protected]> Tue, 10 Feb 2015 16:12:30 +0000
libmaus (0.0.193-1) unstable; urgency=low
* add BamCatHeader constructor method with ArgInfo object
-- German Tischler <[email protected]> Mon, 09 Feb 2015 09:30:08 +0000
libmaus (0.0.192-1) unstable; urgency=low
* extend API by allowing to pass options via ArgInfo object when constructing BamMergeCoordinate and BamMergeQueryName
* add functionality for reading CRAM indexes via callbacks
-- German Tischler <[email protected]> Fri, 30 Jan 2015 15:54:12 +0000
libmaus (0.0.191-1) unstable; urgency=low
* add decompress option for cram input callback setup
-- German Tischler <[email protected]> Thu, 29 Jan 2015 22:57:38 +0000
libmaus (0.0.190-1) unstable; urgency=low
* enable generation of MD and NM fields when decoding CRAM via io_lib
-- German Tischler <[email protected]> Wed, 28 Jan 2015 14:41:27 +0000
libmaus (0.0.189-1) unstable; urgency=low
* add CRAM input via callback interface for io_lib
* add SAM encoder
-- German Tischler <[email protected]> Wed, 28 Jan 2015 09:14:23 +0000
libmaus (0.0.188-1) unstable; urgency=low
* use input stream factories in BAM decoder construction factories
* add iRODS input stream interface
-- German Tischler <[email protected]> Thu, 22 Jan 2015 08:51:27 +0000
libmaus (0.0.187-1) unstable; urgency=low
* use fixed order of attributes when rewriting BAM header lines
-- German Tischler <[email protected]> Fri, 16 Jan 2015 09:07:49 +0000
libmaus (0.0.186-1) unstable; urgency=low
* adding CRC32C digest
* extending number range to [-2^31,2^32-1] when converting SAM to BAM
* adding a minimal/incomplete HDF5 decoding wrapper interface for the hdf5 libs
* adding a method for replacing read group ids in BAM headers
-- German Tischler <[email protected]> Wed, 14 Jan 2015 12:28:10 +0000
libmaus (0.0.185-1) unstable; urgency=low
* update debian packaging files
-- German Tischler <[email protected]> Mon, 01 Dec 2014 09:04:59 +0000
libmaus (0.0.184-1) unstable; urgency=low
* import CRC32C code
* refactoring of libmausdigests library
-- German Tischler <[email protected]> Sun, 30 Nov 2014 17:37:20 +0000
libmaus (0.0.183-1) unstable; urgency=low
* adapt code for compilation using nettle 2.4
-- German Tischler <[email protected]> Fri, 28 Nov 2014 12:34:06 +0000
libmaus (0.0.182-1) unstable; urgency=low
* update debian packaging files
-- German Tischler <[email protected]> Sat, 22 Nov 2014 11:55:03 +0000
libmaus (0.0.181-1) unstable; urgency=low
* fix out of tree build
-- German Tischler <[email protected]> Thu, 20 Nov 2014 15:42:24 +0000
libmaus (0.0.180-1) unstable; urgency=low
* fix compilation for non x86 type platforms
-- German Tischler <[email protected]> Thu, 20 Nov 2014 12:43:47 +0000
libmaus (0.0.179-1) unstable; urgency=low
* make compilation of test programs optional
* fix compilation issues
-- German Tischler <[email protected]> Wed, 19 Nov 2014 19:29:49 +0000
libmaus (0.0.178-1) unstable; urgency=low
* fix bug in left shift operator of UnsignedInteger class
* import assembly code for SHA256 and SHA512 (see AUTHORS file)
-- German Tischler <[email protected]> Tue, 18 Nov 2014 15:10:09 +0000
libmaus (0.0.177-1) unstable; urgency=low
* generalise += operator in UnsignedInteger class for different length operands
-- German Tischler <[email protected]> Fri, 14 Nov 2014 12:30:19 +0000
libmaus (0.0.176-1) unstable; urgency=low
* add Null hash digest for performance testing
* add SingleFileServer class
-- German Tischler <[email protected]> Thu, 13 Nov 2014 13:59:59 +0000
libmaus (0.0.175-1) unstable; urgency=low
* add getWords method in UnsignedInteger class
-- German Tischler <[email protected]> Wed, 12 Nov 2014 14:31:48 +0000
libmaus (0.0.174-1) unstable; urgency=low
* add operator*= and isNull methods in UnsignedInteger class
-- German Tischler <[email protected]> Wed, 12 Nov 2014 08:57:02 +0000
libmaus (0.0.173-1) unstable; urgency=low
* fix library start up lockups due to ordering of static initialisation
-- German Tischler <[email protected]> Mon, 10 Nov 2014 10:24:46 +0000
libmaus (0.0.172-1) unstable; urgency=low
* added sam file parser
* added (template) fixed with unsigned integer class
* added support interface for sha message digests via nettle library
-- German Tischler <[email protected]> Thu, 06 Nov 2014 22:16:43 +0000
libmaus (0.0.171-1) unstable; urgency=low
* fix output flushing in streaming duplicate marking
-- German Tischler <[email protected]> Fri, 24 Oct 2014 07:18:37 +0100
libmaus (0.0.170-1) unstable; urgency=low
* added LineBuffer class
-- German Tischler <[email protected]> Thu, 23 Oct 2014 09:28:26 +0100
libmaus (0.0.169-1) unstable; urgency=low
* update handling of header merging in BamCat class for non streaming mode
-- German Tischler <[email protected]> Wed, 15 Oct 2014 14:16:04 +0100
libmaus (0.0.168-1) unstable; urgency=low
* adding simple local alignment class
* adding algorithm for computing strongly connected components in directed graphs
* adding generic topological sorting algorithm for directed graphs
* adding getSequenceIdByName method in FastAIndex class
-- German Tischler <[email protected]> Mon, 13 Oct 2014 09:11:53 +0100
libmaus (0.0.167-1) unstable; urgency=low
* fix line splitting gzipped output stream
-- German Tischler <[email protected]> Wed, 17 Sep 2014 07:29:20 +0100
libmaus (0.0.166-1) unstable; urgency=low
* add line split output variants in BamToFastqOutputFileSet
-- German Tischler <[email protected]> Tue, 16 Sep 2014 09:56:39 +0100
libmaus (0.0.165-1) unstable; urgency=low
* add line splitting output streams (plain and gzip)
-- German Tischler <[email protected]> Mon, 15 Sep 2014 15:20:47 +0100
libmaus (0.0.164-1) unstable; urgency=low
* add option to put rank on alignment input in streaming bam duplicate marking
-- German Tischler <[email protected]> Tue, 02 Sep 2014 09:58:32 +0100
libmaus (0.0.163-1) unstable; urgency=low
* fixing compilation on freebsd
* add getErrorRate method in local edit distance result
* add shallowMerge method in FastInterval
-- German Tischler <[email protected]> Thu, 28 Aug 2014 21:25:09 +0100
libmaus (0.0.162-1) unstable; urgency=low
* fix chunk merging for range restricted bam decoding
-- German Tischler <[email protected]> Thu, 21 Aug 2014 14:29:48 +0100
libmaus (0.0.161-1) unstable; urgency=low
* add PlainOrGzipStream class
-- German Tischler <[email protected]> Wed, 20 Aug 2014 11:09:37 +0100
libmaus (0.0.160-1) unstable; urgency=low
* avoid x86 specific asm when not compiling for x86 architecture
-- German Tischler <[email protected]> Tue, 19 Aug 2014 14:38:31 +0100
libmaus (0.0.159-1) unstable; urgency=low
* remove usage of gcc builtin for byte swapping
-- German Tischler <[email protected]> Tue, 19 Aug 2014 12:51:15 +0100
libmaus (0.0.158-1) unstable; urgency=low
* fix compilation with glibc 2.4
-- German Tischler <[email protected]> Mon, 18 Aug 2014 09:43:49 +0100
libmaus (0.0.157-1) unstable; urgency=low
* add tag filtering on streaming bam duplicate marking output
-- German Tischler <[email protected]> Fri, 15 Aug 2014 14:34:51 +0100
libmaus (0.0.156-1) unstable; urgency=low
* add setRange method in BamRangeDecoder class
* add addMateTag method in BamAlignment
* add BamBlockWriterBase interface methods in BamStreamingMarkDuplicates
* add tag support in streaming duplicate marking
-- German Tischler <[email protected]> Tue, 12 Aug 2014 21:33:32 +0100
libmaus (0.0.155-1) unstable; urgency=medium
* update packaging files
-- German Tischler <[email protected]> Sun, 10 Aug 2014 21:28:37 +0100
libmaus (0.0.154-1) unstable; urgency=low
* add IntegerInterval class
-- German Tischler <[email protected]> Sat, 09 Aug 2014 16:07:09 +0100
libmaus (0.0.153-1) unstable; urgency=low
* enable parallel writing of temporary files in BamEntryContainer
* add SimpleHashMapInsDel/SimpleHashSetInsDel classes
* add streaming alignment duplicate marking class
* fix several bugs in optical duplicate counting
* add sparse LRU class and file set
* add support methods for streaming duplicate marking in BamAlignment class
* add KmerCache class
-- German Tischler <[email protected]> Mon, 04 Aug 2014 16:28:59 +0100
libmaus (0.0.152-1) unstable; urgency=low
* add support for two output files in duplicate removal
-- German Tischler <[email protected]> Wed, 23 Jul 2014 09:13:49 +0100
libmaus (0.0.151-1) unstable; urgency=low
* refactor GNU TLS interface classes
-- German Tischler <[email protected]> Tue, 22 Jul 2014 09:16:35 +0100
libmaus (0.0.150-1) unstable; urgency=medium
* add GNU TLS interface
-- German Tischler <[email protected]> Mon, 21 Jul 2014 21:56:10 +0100
libmaus (0.0.149-1) unstable; urgency=low
* extend tag in ReadEnds class to 64 bits
-- German Tischler <[email protected]> Fri, 18 Jul 2014 19:55:18 +0100
libmaus (0.0.148-1) unstable; urgency=low
* add infrastructure for tag splitting in duplicate marking
-- German Tischler <[email protected]> Wed, 16 Jul 2014 14:26:41 +0100
libmaus (0.0.147-1) unstable; urgency=low
* versioning cleanup
-- German Tischler <[email protected]> Mon, 14 Jul 2014 10:20:01 +0100
libmaus (0.0.146-1) unstable; urgency=low
* add SimpleTrie class
* improve error message when detecting redirect loop in http(s)
* generalise optical coordinate parsing in ReadEnds (D. Jackson)
-- German Tischler <[email protected]> Mon, 14 Jul 2014 10:05:32 +0100
libmaus (0.0.143-1) unstable; urgency=low
* avoid failing the merging state of collation due to too many open files
by merging through a single file handle if required
-- German Tischler <[email protected]> Thu, 10 Jul 2014 16:51:39 +0100
libmaus (0.0.142-1) unstable; urgency=low
* add sbam input format in alignment decoder factory (bam input via io_lib)
-- German Tischler <[email protected]> Thu, 10 Jul 2014 09:28:20 +0100
libmaus (0.0.141-1) unstable; urgency=low
* fix cram writer instantiation in factory class
-- German Tischler <[email protected]> Tue, 08 Jul 2014 23:26:55 +0100
libmaus (0.0.140-1) unstable; urgency=low
* fix findRG method in BamHeaderLowMemory class
-- German Tischler <[email protected]> Tue, 08 Jul 2014 13:30:10 +0100
libmaus (0.0.139-1) unstable; urgency=low
* fix compilation issues
-- German Tischler <[email protected]> Tue, 08 Jul 2014 09:45:16 +0100
libmaus (0.0.138-1) unstable; urgency=medium
* fix eof detection in HttpBody class
-- German Tischler <[email protected]> Sun, 06 Jul 2014 20:15:53 +0100
libmaus (0.0.137-1) unstable; urgency=low
* add url (http/https/ftp/file) input stream classes
* fix putback region in PosixFdInputStreamBuffer
-- German Tischler <[email protected]> Sun, 06 Jul 2014 19:59:18 +0100
libmaus (0.0.136-1) unstable; urgency=low
* added GeneFlatFile class
* added getUnparsedRestArg method in ArgInfo class
* added IsGzip class
* various compilation fixes
-- German Tischler <[email protected]> Fri, 04 Jul 2014 16:32:52 +0100
libmaus (0.0.135-1) unstable; urgency=low
* fix insallation path of include files
-- German Tischler <[email protected]> Wed, 02 Jul 2014 19:13:10 +0100
libmaus (0.0.134-1) unstable; urgency=low
* change exec flags in packaging
-- German Tischler <[email protected]> Wed, 02 Jul 2014 08:36:08 +0100
libmaus (0.0.133-1) unstable; urgency=low
* reduce memory usage in Chromosome class
-- German Tischler <[email protected]> Tue, 01 Jul 2014 23:31:28 +0100
libmaus (0.0.132-1) unstable; urgency=low
* add BamHeaderLowMem class
-- German Tischler <[email protected]> Tue, 01 Jul 2014 12:43:11 +0100
libmaus (0.0.131-1) unstable; urgency=low
* fix compilation of alignment construction variant in BamWriter
-- German Tischler <[email protected]> Tue, 24 Jun 2014 09:43:04 +0100
libmaus (0.0.130-1) unstable; urgency=low
* add test for pthread_setaffinity_np (instead of checking for linux)
* fix compilation for big endian systems
* do not attempt to build scram decoder if dl functions are missing
* add soft clipping read extraction methods in BamAlignment class
* add sub range extraction for indexed FastA
* improve LCS computation
* support non standard locations for zlib
* add option for disabling AIO classes
* add support for igzip in bgzf compression
* add run-time checks for various instruction sets
* improve help messages
-- German Tischler <[email protected]> Tue, 17 Jun 2014 14:07:33 +0100
libmaus (0.0.129-1) unstable; urgency=medium
* modifications for compilation using glibc < 2.6
-- German Tischler <[email protected]> Sun, 08 Jun 2014 13:06:45 +0100
libmaus (0.0.128-1) unstable; urgency=low
* add check for 128 bit integers
* add compressed HWT based LF variant
* fix compilation on gcc 4.1.2
-- German Tischler <[email protected]> Thu, 05 Jun 2014 09:30:27 +0100
libmaus (0.0.127-1) unstable; urgency=low
* implement streaming mode for bam concatenation
-- German Tischler <[email protected]> Sat, 31 May 2014 17:11:49 +0100
libmaus (0.0.126-1) unstable; urgency=low
* add methods for getting front and back soft clipping of an alignment
-- German Tischler <[email protected]> Tue, 27 May 2014 19:01:28 +0100
libmaus (0.0.125-1) unstable; urgency=low
* add method for removing SQ lines fro a BAM header
-- German Tischler <[email protected]> Fri, 23 May 2014 16:16:39 +0100
libmaus (0.0.124-1) unstable; urgency=low
* fix duplication metrics computation for multiple libraries
-- German Tischler <[email protected]> Sat, 17 May 2014 22:46:15 +0100
libmaus (0.0.122-1) unstable; urgency=low
* add name checking during alignment construction
* add spin lock class based on Darwin API
* add wavelet tree with run length compressed node bit vectors
-- German Tischler <[email protected]> Wed, 14 May 2014 14:57:01 +0100
libmaus (0.0.121-1) unstable; urgency=low
* fix compilation on Darwin
-- German Tischler <[email protected]> Thu, 08 May 2014 10:25:23 +0100
libmaus (0.0.120-1) unstable; urgency=low
* improve CRAM sub range support
-- German Tischler <[email protected]> Wed, 07 May 2014 10:08:46 +0100
libmaus (0.0.119-1) unstable; urgency=low
* add subrange decoding support for cram through io_lib
-- German Tischler <[email protected]> Tue, 06 May 2014 16:41:15 +0100
libmaus (0.0.118-1) unstable; urgency=low
* update bam validation to allow annotation lines in bam file input
-- German Tischler <[email protected]> Thu, 01 May 2014 13:41:03 +0100
libmaus (0.0.117-1) unstable; urgency=low
* implement exception handling in simple thread pool
-- German Tischler <[email protected]> Thu, 01 May 2014 10:18:17 +0100
libmaus (0.0.116-1) unstable; urgency=low
* add insertExtend method in SimpleCountingHash and SimpleHashMap
-- German Tischler <[email protected]> Tue, 29 Apr 2014 16:36:08 +0100
libmaus (0.0.115-1) unstable; urgency=medium
* implement MD/NM calculation for BAM sorting output
-- German Tischler <[email protected]> Fri, 18 Apr 2014 23:01:31 +0100
libmaus (0.0.114-1) unstable; urgency=medium
* import CRC32 code by Stephan Brumme
* avoid excessive amount of flush operations while creating wavelet tree for large alphabet RLE data
* extend BamAlignmentDecoderBase API for with method for outputting original quality instead of quality field when converting to FastQ
-- German Tischler <[email protected]> Fri, 18 Apr 2014 21:14:21 +0100
libmaus (0.0.113-1) unstable; urgency=low
* fix compilation on Darwin
-- German Tischler <[email protected]> Mon, 14 Apr 2014 21:58:04 +0100
libmaus (0.0.112-1) unstable; urgency=low
* fix compilation without optimisation flags
-- German Tischler <[email protected]> Thu, 10 Apr 2014 20:11:53 +0100
libmaus (0.0.111-1) unstable; urgency=low
* add RAZF file format decoder
* add FastA (.fai) index decoder
-- German Tischler <[email protected]> Thu, 10 Apr 2014 17:52:17 +0100
libmaus (0.0.110-1) unstable; urgency=low
* bug/warning fixes
* add number formatting function in ArgInfo class
-- German Tischler <[email protected]> Thu, 03 Apr 2014 13:55:42 +0100
libmaus (0.0.109-1) unstable; urgency=low
* add simplified thread pool
* add posix spin lock class
* refactor parallel stable sorting for use in thread pools
* add zlib compressor/decompressor objects for simple compressed i/o
* extend search options in BidirectionalDnaIndexTemplate
* add block wise compressed file input for use in thread pools
* do not use O_NOATIME by default when opening files based on posix api
* add parallel bam sorting test program
-- German Tischler <[email protected]> Wed, 02 Apr 2014 09:22:26 +0100
libmaus (0.0.108-1) unstable; urgency=low
* fix PosixFdOutputStream construction by file name
-- German Tischler <[email protected]> Wed, 19 Mar 2014 09:13:45 +0000
libmaus (0.0.107-1) unstable; urgency=low
* added gap array variant using one byte per index plus overflow buffer
-- German Tischler <[email protected]> Tue, 18 Mar 2014 09:46:19 +0000
libmaus (0.0.106-1) unstable; urgency=low
* add pseudo random access bgzf input stream
* make posix fd based input stream seekable
-- German Tischler <[email protected]> Thu, 06 Mar 2014 13:58:25 +0000
libmaus (0.0.105-1) unstable; urgency=low
* add computation of MD/NM aux fields for BamAlignment
-- German Tischler <[email protected]> Sun, 02 Mar 2014 18:32:12 +0000
libmaus (0.0.104-1) unstable; urgency=low
* add meta information in BAM indexing
-- German Tischler <[email protected]> Fri, 21 Feb 2014 09:15:16 +0000
libmaus (0.0.103-1) unstable; urgency=low
* fixes for linear part of BAM indexing
-- German Tischler <[email protected]> Thu, 20 Feb 2014 12:42:54 +0000
libmaus (0.0.102-1) unstable; urgency=low
* add method for setting the mapping quality field in a BamAlignment object
-- German Tischler <[email protected]> Wed, 12 Feb 2014 09:46:01 +0000
libmaus (0.0.101-1) unstable; urgency=low
* API extension in BamAuxFilterVector class
-- German Tischler <[email protected]> Tue, 11 Feb 2014 19:27:50 +0000
libmaus (0.0.100-1) unstable; urgency=low
* use new compressed stream infrastructre in BamEntryContainer
-- German Tischler <[email protected]> Tue, 11 Feb 2014 15:49:40 +0000
libmaus (0.0.99-1) unstable; urgency=low
* improve handling of empty bgzf blocks
-- German Tischler <[email protected]> Fri, 31 Jan 2014 12:32:39 +0000
libmaus (0.0.98-1) unstable; urgency=low
* add putFastA method in BamAlignmentDecoderBase
-- German Tischler <[email protected]> Sun, 26 Jan 2014 12:39:12 +0000
libmaus (0.0.97-1) unstable; urgency=low
* extend Pattern class in fastx namespace with line oriented printing methods
-- German Tischler <[email protected]> Mon, 20 Jan 2014 09:01:22 +0000
libmaus (0.0.96-1) unstable; urgency=low
* extend BamAlignment for allowing reset operations on raw alignment blocks
-- German Tischler <[email protected]> Sun, 05 Jan 2014 17:11:43 +0000
libmaus (0.0.95-1) unstable; urgency=low
* no change version bump to set up experimental branch in libmaus-debian
-- German Tischler <[email protected]> Thu, 12 Dec 2013 16:22:34 +0000
libmaus (0.0.94-1) unstable; urgency=low
* add methods for mate pair information fixing in BamAlignment class
-- German Tischler <[email protected]> Thu, 12 Dec 2013 15:55:49 +0000
libmaus (0.0.93-1) unstable; urgency=low
* fix compilation
-- German Tischler <[email protected]> Fri, 29 Nov 2013 15:17:23 +0000
libmaus (0.0.92-1) unstable; urgency=low
* add getReadGroup function in BamAlignmentDecoderBase
-- German Tischler <[email protected]> Fri, 29 Nov 2013 14:06:59 +0000
libmaus (0.0.91-1) unstable; urgency=low
* add gz option in bamtofastq output stream container class
-- German Tischler <[email protected]> Thu, 14 Nov 2013 19:36:45 +0000
libmaus (0.0.90-1) unstable; urgency=low
* add generic buffered gzip output stream class
-- German Tischler <[email protected]> Thu, 14 Nov 2013 16:58:00 +0000
libmaus (0.0.89-1) unstable; urgency=low
* fix BAM merging crashes
-- German Tischler <[email protected]> Fri, 08 Nov 2013 13:11:00 +0000
libmaus (0.0.88-1) unstable; urgency=low
* fix BAM indexing
-- German Tischler <[email protected]> Wed, 06 Nov 2013 12:42:51 +0000
libmaus (0.0.87-1) unstable; urgency=low
* add alignment reading factory class
* fixes for BAM writing
-- German Tischler <[email protected]> Mon, 04 Nov 2013 20:50:13 +0000
libmaus (0.0.86-1) unstable; urgency=low
* add alignment writer factory class
-- German Tischler <[email protected]> Sun, 03 Nov 2013 18:07:08 +0000
libmaus (0.0.85-1) unstable; urgency=low
* add block write callback parameter in BamEntryContainer's output production course
-- German Tischler <[email protected]> Wed, 30 Oct 2013 09:36:11 +0000
libmaus (0.0.84-1) unstable; urgency=low
* add HuffmanTree class
-- German Tischler <[email protected]> Tue, 29 Oct 2013 13:52:11 +0000
libmaus (0.0.83-1) unstable; urgency=low
* extend API in bambam namespace with duplicate marking code
-- German Tischler <[email protected]> Mon, 28 Oct 2013 12:08:43 +0000
libmaus (0.0.82-1) unstable; urgency=low
* add block output callback in BgzfRecode
* add callback passing in BamParallelRewrite
-- German Tischler <[email protected]> Sat, 26 Oct 2013 00:08:39 +0100
libmaus (0.0.81-1) unstable; urgency=low
* add pointer types for bgzf/BAM callbacks and digest saving
-- German Tischler <[email protected]> Fri, 25 Oct 2013 21:41:15 +0100
libmaus (0.0.80-1) unstable; urgency=low
* add bgzf/BAM output callbacks for MD5 and BAM indexing
-- German Tischler <[email protected]> Fri, 25 Oct 2013 20:39:22 +0100
libmaus (0.0.79-1) unstable; urgency=low
* fix BAM read group processing in merging
-- German Tischler <[email protected]> Fri, 25 Oct 2013 08:49:02 +0100
libmaus (0.0.78-1) unstable; urgency=low
* set sort order in BamMergeTemplate class according to input data
-- German Tischler <[email protected]> Thu, 24 Oct 2013 09:12:09 +0100
libmaus (0.0.77-1) unstable; urgency=low
* add BAM merging code
-- German Tischler <[email protected]> Tue, 22 Oct 2013 13:43:23 +0100
libmaus (0.0.76-1) unstable; urgency=low
* add FSM based BAM header parsing
-- German Tischler <[email protected]> Thu, 17 Oct 2013 09:36:51 +0100
libmaus (0.0.75-1) unstable; urgency=low
* fix BamWriter destruction crashes due to wronger pointer types
-- German Tischler <[email protected]> Thu, 03 Oct 2013 22:23:20 +0100
libmaus (0.0.74-1) unstable; urgency=low
* add default cache line size for older linux systems
-- German Tischler <[email protected]> Wed, 02 Oct 2013 09:44:16 +0100
libmaus (0.0.73-1) unstable; urgency=low
* API extensions (ReadEnds comparator class, BamAlignment)
-- German Tischler <[email protected]> Wed, 02 Oct 2013 08:41:43 +0100
libmaus (0.0.72-1) unstable; urgency=low
* check for availability of MSG_CMSG_CLOEXEC in configure
-- German Tischler <[email protected]> Thu, 26 Sep 2013 21:40:46 +0100
libmaus (0.0.71-1) unstable; urgency=low
* fix compilation on Darwin, make code compile with clang
-- German Tischler <[email protected]> Mon, 16 Sep 2013 13:53:42 +0100
libmaus (0.0.70-1) unstable; urgency=low
* add searchCompleteNoFailureZ method for LinearHashTrie class
-- German Tischler <[email protected]> Mon, 09 Sep 2013 11:58:36 +0100
libmaus (0.0.69-1) unstable; urgency=low
* add range restricted collating BAM decoding
-- German Tischler <[email protected]> Fri, 30 Aug 2013 11:48:00 +0100
libmaus (0.0.68-1) unstable; urgency=low
* update checking of the observed template length to new SAM specs
-- German Tischler <[email protected]> Wed, 07 Aug 2013 12:39:15 +0100
libmaus (0.0.67-1) unstable; urgency=low
* update position checking according to new SAM specification
-- German Tischler <[email protected]> Wed, 07 Aug 2013 11:33:04 +0100
libmaus (0.0.66-1) unstable; urgency=low
* add next0 function to bitbtree
* improve Hamming distance based overlap detection
-- German Tischler <[email protected]> Mon, 05 Aug 2013 09:47:53 +0100
libmaus (0.0.65-1) unstable; urgency=low
* add BamHeaderRewriteCallback class for BamParallelRewrite
-- German Tischler <[email protected]> Fri, 02 Aug 2013 11:41:16 +0100
libmaus (0.0.64-1) unstable; urgency=low
* add BamParallelRewrite class
-- German Tischler <[email protected]> Thu, 01 Aug 2013 13:47:17 +0100
libmaus (0.0.63-1) unstable; urgency=low
* fix BgzfInflate class
-- German Tischler <[email protected]> Wed, 31 Jul 2013 13:45:51 +0100
libmaus (0.0.62-1) unstable; urgency=low
* added BamRangeDecoder class
-- German Tischler <[email protected]> Wed, 31 Jul 2013 12:16:22 +0100
libmaus (0.0.61-1) unstable; urgency=low
* add BamRange classes
* use CheckedInputStream for blockwise snappy input
-- German Tischler <[email protected]> Mon, 29 Jul 2013 20:27:48 +0100
libmaus (0.0.60-1) unstable; urgency=low
* add BamIndex class
* add level based gamma coding based gap file set class
-- German Tischler <[email protected]> Wed, 24 Jul 2013 09:51:00 +0100
libmaus (0.0.59-1) unstable; urgency=low
* print correct error message when fork() call fails
* parameterise edge array in overlap computation
* refactor serialisation function in AutoArray class (factor out header writing)
* terminate queue in case of async input failure in AsynchronousSocketInputBuffer
* add read method in ReorderConcatGenericInput class
* make construction of CompactReadEndContainer class more verbose
* add class for scram encoding (cram+sam output via io_lib)
* add pseudo random position input for compact fasta files
* add verbosity for Hamming distance based overlap detection
* add function readPlusInfo in BgzfInflate class which returns size of compressed
data in addition to uncompressed one (for BAM indexing)
* add parallel sorting option in PairFileSorting class
* add sparse gamma code based gap file class and tests
* fix edge list terminator in EdgeList class
* add function for recomputing the bin of a BAM alignment block
-- German Tischler <[email protected]> Mon, 22 Jul 2013 13:40:46 +0100
libmaus (0.0.58-1) unstable; urgency=low
* add getAdapterMatchFreqs function to adapter finding class
-- German Tischler <[email protected]> Fri, 05 Jul 2013 10:42:05 +0100
libmaus (0.0.57-1) unstable; urgency=low
* bump version after API changes in bambam namespace
-- German Tischler <[email protected]> Thu, 04 Jul 2013 11:31:51 +0100
libmaus (0.0.56-1) unstable; urgency=low
* bump version after fixing locking in bloom filter class
-- German Tischler <[email protected]> Tue, 02 Jul 2013 21:59:20 +0100
libmaus (0.0.55-1) unstable; urgency=low
* bump version after API extensions in bambam namespace
-- German Tischler <[email protected]> Wed, 26 Jun 2013 12:28:01 +0100
libmaus (0.0.54-1) unstable; urgency=low
* bump version after fixing compilation on 32 bit machines
-- German Tischler <[email protected]> Fri, 21 Jun 2013 14:40:20 +0100
libmaus (0.0.53-1) unstable; urgency=low
* bump version after adding pointer types
-- German Tischler <[email protected]> Fri, 21 Jun 2013 09:19:58 +0100
libmaus (0.0.52-1) unstable; urgency=low
* bump version after fixing crash due to non transitive order in previous bam alignment name comparison
-- German Tischler <[email protected]> Thu, 20 Jun 2013 09:59:02 +0100
libmaus (0.0.51-1) unstable; urgency=low
* bump version after using static functions instead of constants for bgzf parameters
-- German Tischler <[email protected]> Wed, 05 Jun 2013 12:10:04 +0100
libmaus (0.0.50-1) unstable; urgency=low
* added combined parallel bgzf inflation/deflation class
-- German Tischler <[email protected]> Mon, 03 Jun 2013 19:35:44 +0100
libmaus (0.0.49-1) unstable; urgency=low
* more API changes in bambam namespace
-- German Tischler <[email protected]> Sat, 01 Jun 2013 22:36:03 +0100
libmaus (0.0.48-1) unstable; urgency=low
* some API changes in bambam namespace
-- German Tischler <[email protected]> Fri, 31 May 2013 15:47:58 +0100
libmaus (0.0.47-1) unstable; urgency=low
* bump version after fixing a division by zero in the DuplicationMetrics class
-- German Tischler <[email protected]> Thu, 30 May 2013 15:10:14 +0100
libmaus (0.0.46-1) unstable; urgency=low
* bump version after fixing ReadEndsContainer class for gcc 4.8
-- German Tischler <[email protected]> Thu, 30 May 2013 10:37:40 +0100
libmaus (0.0.45-1) unstable; urgency=low
* bump version after adding a function to the ReadEndsContainer class
-- German Tischler <[email protected]> Thu, 23 May 2013 11:55:00 +0100
libmaus (0.0.44-1) unstable; urgency=low
* bump version after importing code
-- German Tischler <[email protected]> Wed, 22 May 2013 14:51:13 +0100
libmaus (0.0.43-1) unstable; urgency=low
* bump version after bambam api changes
-- German Tischler <[email protected]> Tue, 21 May 2013 07:07:16 +0100
libmaus (0.0.42-1) unstable; urgency=low
* bump version after adding parallel bam file decoding
-- German Tischler <[email protected]> Fri, 17 May 2013 11:37:41 +0100
libmaus (0.0.41-1) unstable; urgency=low
* bump version after adding function for disabling validation in collating bam decoder
-- German Tischler <[email protected]> Thu, 09 May 2013 11:50:20 +0100
libmaus (0.0.40-1) unstable; urgency=low
* bump version after changing parameter order in collation class