Fix building without TBB Malloc library (:issue:`98`)

Fix rounding error in lca classifier (:issue:`93`)

allow multiple output types at once

add dedicated CSV/TSV output (:issue:`10`)

fix loading reference database from running ARB (:issue:`76`)

report errors when sequence can't be read from ARB (:issue:`73`)

add :option:`--arb-list-fields` listing fields available in ARB database

fix progress bar not honoring verbosity (:issue:`85`)

make internal kmer engine the default (:issue:`23`)

add pretty progress monitor

run search stage in parallel (:issue:`32`)

:option:`--num-pts` defaults to number of cores available (previous: 1)

add :option:`--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 :option:`--fs-oldmatch` for old implementation)

replace boost::mutex with std::mutex (c++11)

fix :option:`--show-dist` if alignment width don't match

fix race starting pt servers (library code not threadsafe)

fix engine type not shown in :option:`--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 :option:`--search` and :option:`--turn`)

update documentation (:issue:`20`)

reinstate :option:`--show-dist`

reinstate :option:`--fs-msc-max`

add choice exact to :option:`--search-iupac`

change default for :option:`--search-kmer-len` to match :option:`--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 (:issue:`25`)

process sequences in parallel (:issue:`17`, :issue:`31`)

add support for gzipped read/write (:issue:`29`)

add support for "-" to read/write using pipes

remove internal pipeline in favor of TBB

add :option:`--add-relatives`; adding search result to output (:issue:`19`)

add logging with variable verbosity (:issue:`14`)

be smart about locating arb_pt_server binary (:issue:`30`)

report number of references discarded due to configured constraints

fix crash if no acceptable references found for a query

fix :option:`--search` causes a program option error (:issue:`28`)

fix race condition in terminating PT server

build binary releases for macOS and Linux (:issue:`26`)

fix "search.h" missing in source tar ball (:issue:`27`)

add option :option:`--fasta-write-dots`; writes dots on edges

add option :option:`--fasta-write-dna`; writes T/t instead of U/u (:issue:`24`)

fix PT server fails to build if ARBHOME not set (:issue:`15`)

fix psina not installed to $bindir

fix tab character in sequence causes sequence to be skipped (:issue:`21`)

fix last line of input FASTA ignored if missing newline (:issue:`16`)

fix :option:`--db` parameter demanded even if not required due to use of :option:`--prealigned`

fix SIGPIPE race on PT server shutdown (:issue:`11`)

split :option:`--help` into "common" and advanced options (:option:`--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 :option:`--help` (:issue:`9`)

added README.md (:issue:`5`)

fix :option:`--fs-req` was ignored

added option :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 :option:`--min-idty` IDTY Excludes sequences with align_slv_idty < IDTY from FASTA output. Implies :option:`--calc-idty`.

added option :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 :option:`--fs-cover-gene` to 0 (faster) The cover-gene feature only makes sense if :option:--gene-start` and :option:`--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 :option:`--ptport` and :option:`--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 :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 :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 :option:`--search-iupac`, :option:`--search-correction` and :option:`--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)