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version.inc
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version.inc
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#define VERSION "1.9.8"
// 1.9.8 10/28/2022 -std=gnu++17
// 1.9.7 07/06/2022 there may be 1 indiscernible object
// 1.9.6 10/18/2021 distTree_inc_refresh_dissim.sh
// 1.9.5 07/23/2021 -prefer_gain is restored in tree2names.sh
// 1.9.4 06/09/2021 combine_dissims.cpp: -barrier
// 1.9.3 05/30/2021 align.cpp: ambiguous aa J,U,O are replaced by X, selfScore is using X
// -prefer_gain is removed
// 1.9.2 05/18/2021 optimizeReinsert() invokes optimizeLargeSubgraphs(&changes)
// 1.9.1 05/15/2021 inc/threads
// distTree_inc_new.sh -reinsert does not process inc/new/
// 1.8.1 05/11/2021 inc/dissim_full
// 1.7.3 04/23/2021 combine_dissims.cpp: weighted combination of all dissimilarities
// str2real() bug in reading nan's
// 1.7.2 04/19/2021 d_{CDS,PRT}: arithmetic average is used
// reinsert: sort by Change::arcDist decsending
// 1.7.1 04/08/2021 inc/indiscern: pairs of indiscernible objects
// hybrids are identified for indiscernibility classes
// getMissingLeafPairs_ancestors(): only for the member with smallest name of an indiscernibility class
// inc/good
// 1.6.2 04/06/2021 makeDistTree: hybrid removal: neighbors are optimized only at the last subgraph optimization iteration
// -delete_deformation_outliers: deformation pair and deformation value are saved
// 1.6.1 03/31/2021 inc/: request2dissim.sh -> pairs2dissim.sh
// request_closest.sh -> object2closest.sh
// request_closest_sql -> object2closest.sql
// grid_min -> pairs2dissim.grid and object2closest.grid
// 1.5.10 03/25/2021 inc/request_closest.sh $OBJ may return $OBJ
// 1.5.9 03/24/2021 NewLeaf::saveRequest() prints empty list of requests if location.indiscernible()
// 1.5.8 03/22/2021 makeDistTree: quality calculation uses threads
// 1.5.7 03/21/2021 FeatureTree::globalSingletonsSize bug
// 1.5.6 03/17/2021 feature tree: only-optional features are removed;
// Genome::coreNonSingletons does not include optionalCore[]
// oneFeatureInTree => Genome::coreSet has no optional nominal attributes
// use threads
// 1.5.5 02/28/2021 DTNode::mtx, Subgraph::subPaths2tree() uses threads
// 1.5.4 02/25/2021 combine_dissims.cpp: linear combination
// d_symbet
// 1.5.3 02/24/2021 reinsert: arcDist >= max ((size_t) log (name2leaf. size () + 1), areaRadius_std)
// 1.5.2 02/15/2021 PositiveAverageModel::ignoreZero
// 1.5.1 01/31/2021 inc/request_closest.sh has 2 parameters; inc/qc_object.sh
// 1.4.2 01/28/2021 distTree_inc_new_log.sh
// 1.4.1 01/24/2021 inc/{large,request_closest_sql} /dev/null or absent
// 1.3.2 01/10/2021 GeneMark2CDS prints incomplete and ambiguous proteins as well
// 1.3.1 12/18/2020 inc/phen_large --> inc/large; inc/request_closest_sql
// 1.2.3 10/03/2020 makeDistTree does not stop on criterion increase of dissimilarity types > 1
// 1.2.2 08/28/2020 distTree_new.cpp accepts a tree file as input
// 1.2.1 08/20/2020 request2dissim.sh: 4 parameters
// 1.1.12 07/28/2020 Newick import removes transient nodes; printDistTree: 'itree' --> 'dm'
// 1.1.11 07/27/2020 improvement of Func::findZero(); statDistTree: length precision is increased; DistTree::saveFeatureTree(withTime); Feature::getLambda()
// 1.1.10 07/18/2020 makeDistTree -min_arc_prob; DistTree::reroot() does not use 3*SD
// 1.1.9 06/23/2020 DistTree::mergeDissimAttrs() bug affecting indiscernibles
// 1.1.8 06/21/2020 variance_min > 0 => indiscernibles are used, otherwise max_degree is very large
// 1.1.7 06/20/2020 compbine_dissims.cpp: swap(name1,name2)
// 1.1.6 06/17/2020 inc/GenBank/ -> inc/genome/, inc/marker/ -> inc/rRNA/
// 1.1.5 06/16/2020 inc/ contains: server, database, bulk, bulk_remote
// 1.1.4 06/11/2020 distTree_inc_save.sh: inc/*.sh are usable for users
// 1.1.3 06/10/2020 distTree_inc_complete.sh: #3 (update database) parameter is removed
// 1.1.2 06/09/2020 distTree_inc_new.sh: ADD = max($OBJS * $RATE, 1)
// 1.1.1 06/05/2020 [ 1 == 1 ] -> true; [ 1 == 0 ] -> false
// 1.1.0 06/03/2020 inc/request_closest.sh: output is 1 column
// 1.0.2 06/02/2020 cpp/genetics/, cpp/dissim/
// 0.0.0 05/11/2020 align.cpp: DNA: gap_open = -1 (was: 0)
// 0.0.0 05/03/2020 Genome.surveillance = 1: -> dead
// 0.0.0 03/04/2020 uniColl..Genogroup2outliers: "update Genome set genogroup = null" before setting Genome.genogroup
// 0.0.0 02/28/2020 bacteria genomes: BUSCO.10, variance power = 4.0, root at 2780458:5196388 (Thermotogae, not Terabacteria group, cf. 16S tree)
// 0.0.0 02/13/2020 extractFastaProt -replace: print all replacements
// 0.0.0 02/12/2020 hmmsearch2besthits.cpp: print all HMMs (which may hit the same proteins)
// 0.0.0 01/10/2020 update Taxroot set hashes_max = 150000 where id = 4751 and hashes_max = 30000;
// 0.0.0 11/06/2019 dbo.TaxLineage and phen/ files are added ' [TYPE_SPECIES]'
// 0.0.0 10/01/2019 distTree_inc.sh: -reinsert is removed
// 0.0.0 09/30/2019 GenBank/: hashed directores: genome, phen; inc/phen_large
// 0.0.0 09/26/2019 panfs/marker/.../inc/request_closest.sh: BLAST output is ordered by nident instead of e-value
// 0.0.0 09/01/2019 distTree_inc_new.sh: makeDistTree -reinsert
// 0.0.0 09/01/2019 better optimization for weights \sim 0
// 0.0.0 09/01/2019 Genogroup2outliers: p-value is lowered (two-tail test): Genome.genogroup_outlier is set to null
// 0.0.0 09/01/2019 normalized object criterion; normalized arc error density
// 0.0.0 09/01/2019 hybrid2db.sh, db2unhybrid.sh: obsolete; Genome.outlier = 'auto_hybrid': redo
// 0.0.0 08/20/2019 findHybrids(): only reliable decisions are left; no unhybrid'ing