Version 1.7.2:

  • Fix building without TBB Malloc library (#98)

Version 1.7.1:

  • Fix rounding error in lca classifier (#93)

Version 1.7.0:

  • allow multiple output types at once
  • add dedicated CSV/TSV output (#10)
  • fix loading reference database from running ARB (#76)
  • report errors when sequence can’t be read from ARB (#73)
  • add --arb-list-fields listing fields available in ARB database

Version 1.6.1:

  • fix progress bar not honoring verbosity (#85)

Version 1.6.0:

  • make internal kmer engine the default (#23)
  • add pretty progress monitor
  • run search stage in parallel (#32)
  • --num-pts defaults to number of cores available (previous: 1)
  • add --search-engine setting search engine for search module
  • always run internal engine without thread limit
  • split num pt servers evently between search and align
  • use fixed point format for logging (instead of scientific format)
  • rewrote family selection (use --fs-oldmatch for old implementation)
  • replace boost::mutex with std::mutex (c++11)
  • fix --show-dist if alignment width don’t match
  • fix race starting pt servers (library code not threadsafe)
  • fix engine type not shown in --show-conf
  • fix writing to ARB sequence cache not threadsafe
  • use lock free map for ARB sequence cache (speedup)
  • add pod buffer to replace std::vector (speedup)
  • add FIFO cache for kmer search results (speedup for --search and --turn)

Version 1.5.0:

  • update documentation (#20)
  • reinstate --show-dist
  • reinstate --fs-msc-max
  • add choice exact to --search-iupac
  • change default for --search-kmer-len to match --fs-kmer-len
  • parallelize launch of background PT servers
  • lower memory usage: - avoid redundant sequence caching by libARBDB - use compact aligned base (50% on internal sequence cache)
  • improve internal kmer search performace - add caching of kmer index on disk - parallelize kmer index construction - add presence/absence optimization
  • fix field align_ident_slv added for 100% matches even when not enabled
  • fix crash on overhang past alignment edge
  • fix libARBDB writing to stdout, clobbering sequence output
  • fix out-of-bounds access on iterator in NAST implementation
  • remove dependency on boost serialization library
  • build release binaries with GCC 7 and C++11 ABI
  • add integration tests watching for accuracy regressions (#25)

Version 1.4.0:

  • process sequences in parallel (#17, #31)
  • add support for gzipped read/write (#29)
  • add support for “-” to read/write using pipes
  • remove internal pipeline in favor of TBB
  • add --add-relatives; adding search result to output (#19)
  • add logging with variable verbosity (#14)
  • be smart about locating arb_pt_server binary (#30)

Version 1.3.5:

  • report number of references discarded due to configured constraints
  • fix crash if no acceptable references found for a query
  • fix --search causes a program option error (#28)
  • fix race condition in terminating PT server

Version 1.3.4:

  • build binary releases for macOS and Linux (#26)
  • fix “search.h” missing in source tar ball (#27)

Version 1.3.3:

  • add option --fasta-write-dots; writes dots on edges
  • add option --fasta-write-dna; writes T/t instead of U/u (#24)
  • fix PT server fails to build if ARBHOME not set (#15)
  • fix psina not installed to $bindir
  • fix tab character in sequence causes sequence to be skipped (#21)
  • fix last line of input FASTA ignored if missing newline (#16)
  • fix --db parameter demanded even if not required due to use of --prealigned
  • fix SIGPIPE race on PT server shutdown (#11)

Version 1.3.2:

  • split --help into “common” and advanced options (--help-all)
  • add psina wrapper script (runs parallel instances of SINA to align a single FASTA file)
  • fix memory access failure in cseq
  • fix memory access failure in mseq
  • fix crash on all references removed by filters
  • don’t exit(1) on --help (#9)
  • added (#5)

Version 1.3.1:

  • add OSX support
  • change license to GPL
  • remove limitation on ARB integration mode
  • move revisioning to git
  • fix compilation with CLANG

Version 1.3.0:

  • dropped support for ARB 5.x

Version 1.2.13:

  • uppercase aligned bases if lowercase=unaligned
  • fix manual typos (thx to Mohamed El-hadidi)
  • search-db defaults to pt-db
  • search-port defaults to pt-port if search/align DBs are identical fixes unnecessary start of two PT servers (thx to Christian Wurzbacher)
  • change default for lca-quorum to 0.7
  • change default for search-min-sim to 0.7
  • be smarter about recoginizing FASTA format files and creating output FASTA name (“.frn”, “.fna”, “.fas”, “/dev/stdin” as input, “.fasta.aligned” and “/dev/stdout” as output)
  • write sequence ID in first column of CSV output
  • add fasta-block and fasta-idx options allowing to process only specific smaller blocks of larger fasta files (for parallelization)

Version 1.2.12:

  • use same ARB field type for align_ident_slv as SILVA uses
  • skip sequences with non-IUPAC characters when building reference and when loading sequences to be aligned from ARB file (complaint is issued on stderr)

Version 1.2.11:

  • fix --fs-req was ignored
  • added option --calc-idty Computes the minimum identity of the aligned query sequence with any of the reference sequences used for alignment. The value is exported in align_slv_idty.
  • added option --min-idty IDTY Excludes sequences with align_slv_idty < IDTY from FASTA output. Implies --calc-idty.

Version 1.2.10:

  • added option --fs-no-graph Uses a column profile with PSP score as template (instead of the POA method) This feature is merely for completeness sake and evaluation. With SILVA SSU the POA based method is much more accurate.
  • changed default for --fs-cover-gene to 0 (faster) The cover-gene feature only makes sense if :option:–gene-start` and --gene-end are set such that the reference actually contains sequences touching these boundaries. If this is not the case, the reference selection algorithm wastes time with a futile search.
  • use unix socket as default for --ptport and --search-port Using “/tmp/sina_<PID>.socket” is a more suitable default than “localhost:4040”, as it runs less risk of accessing a different PT server than intended.
  • fix inconsistencies in generated meta data fields and log output
  • updated ARB components to SVN revision 8225
  • added option --write-used-rels The field used_rels is interpreted by ARB as the field containing the reference sequences that were used during alignment.
  • no longer write full_name content when exporting meta data encoded in the FASTA header
  • re-add clamped align_quality_slv
  • fix score normalization (scores > 1 were possible when fs-weight > 0)
  • fix calculation of bp score when orig-db no set (default ptdb)
  • added option --fs-req-gaps n Ignores reference sequences having less than n gaps before the last base. I.e.: Ignores “unaligned” sequences. This is useful when running SINA out of ARB to prevent accidental alignment against unaligned sequences.
  • added options --search-iupac, --search-correction and --search-cover These options configure how the “distance” (identity, similarity, …) is calculated.
  • skip FASTA input sequences that contain invalid characters (i.e. not IUPAC encoded bases, ‘.’, ‘-‘ or white space)

Version 1.2.9:

  • fixed sequence not filled with gap characters after copying full alignment

Version 1.2.8:

  • made –extra-fields actually load multiple fields from arb file
  • fixed sequence not filled with gap characters after copying subalignment
  • updated ARB components to SVN revision 7985
  • added changelog :)