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Vidjil-algo

[!note] This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil platform.

Algo 2026-06⚓︎

  • Added support for WASM !1708
  • Improved read count approximation in input FASTA files !1715
  • The start and end positions of framework and complimentary-determining regions (FRs & CDRs) located on clonotypes are now output in .vidjil and .tsv files, along with possible warnings if their length is abnormal #1841, !1730
  • Fixed AIRR's .tsv CDR3 start and end field names !1733
  • When no clone was found during analysis or --no-vidjil was passed through the command line, an empty array ([]) is now output instead of null #1773, !1740
  • Fixed occasionally off-by-1 CDR3 / JUNCTION positions !1726
  • More recent g++ & clang++ compiler versions are now tested with vidjil-algo !1757
  • Fixed missing key for unexpected germline #5459, !1758
  • The minimum required coverage to compute the consensus sequence can now be configured through the command line with --min-coverage-consensus #5419, !1756
  • K-mers extracted from genes to search for that are common with those from genes not to search for on reads are now systematically removed from the index, yielding more accurate results #5436, !1748

Algo 2025-12⚓︎

  • Vidjil-algo behaviour is now similar to the release 2024-02, but still benefiting from the speedup (#5429 #5434)
  • Fix the export of affect values (#5437 #5465)
  • Fix computation of gene border positions (do not take into account upstream/downstream regions as being within the gene anymore, #5237). This fixes some issues with productivity computation.

Algo 2025-02⚓︎

  • Large refactor, one-pass Aho-Corasick automaton (!1527)
  • This brings up to 3-5x speed-ups on detecting multiple loci --filter
  • --filter outputs .fastq files, with sequence quality, when the input is .fastq
  • Note that -2 and --find options are not working in this release
  • For capture and RNA-Seq data, it is advised now to stay on release 2024.02 (except for --filter)

Algo 2024-02-02⚓︎

  • New option --top-by-locus, reporting a minimum number of clonotypes per recombination system !1335
  • Improved .json output, with number of clones by locus !1146
  • Use global similarity for similarity matrix computation !1284

Algo 2022-03-14⚓︎

  • Fix a regression from the previous release, correctly handling absolute paths in germlines !1144

Algo 2022-02-21⚓︎

  • New option --find to detect and align sequences without recombinations !1004
  • Diversity measures also reported by locus !1111, Pielou's evenness index correctly named !1132
  • Report not designated sequences as "Possibly", new warning W68 !1008
  • Refactor, streamlining germline handling/declaration !1010 :xxx filter works with several -g / mix of -g / -V/-D/-J / --find
  • Update third-party libraries (CLI11, json, see also doc/LICENSE.md) !1036 !1123
  • New Docker framework to run tests #4203
  • Update test framework !669, faster tests launching at once .should-vdj tests !413
  • New support policy for compilers, gcc >= 7.5, clang >= 6.0, support also gcc 11, clang 12 !1005 !1128
  • Bugs closed #4425 #4775
  • New and updated documentation, roadmap, and credits

Algo 2021-04-28⚓︎

  • New unproductivity cause, reporting IGH sequences without a {WP}GxG pattern !935
  • Updated germlines from IMGT/GENE-DB, as well with 60bp up/downstream !885 !892
  • Included Sus Scrofa and Gallus Gallus germlines !478 !839
  • JUNCTION/CDR3 analysis by default, deprecating -3 option !947
  • Smaller --max-consensus output, without debug information, new advanced option --out-details !724
  • Updated outputs (e-values, affects) !932
  • New and updated documentation and online help

Algo 2021-02-18⚓︎

  • New preset --filter-reads to filter potentially huge datasets (vidjil.cpp) #4681
  • Better --gz option, outputting also .fa.gz and .affects.gz files (vidjil.cpp) #4692
  • New and updated documentation

Algo 2021-02-05⚓︎

  • New report of unproductivity causes in 'seg.junction.unproductive' (core/segment.cpp) #4599
  • New fields in AIRR .tsv output, 'vj_in_frame', 'stop_codon', '{v,j}support', '{v,d,j,cdr3}_sequence' (core/output.cpp) #3569 #4643
  • Ability to get the input reads from stdin with '-' (core/fasta.cpp) #4642
  • New advanced option --read-number to override e-value multiplier, new warning W21 on doubtful multipliers (vidjil.cpp) !887
  • New experimental option --show-junction, displaying germline genes on stdout (core/segment.cpp) !886
  • Bugs closed (W61 warning check)
  • New and updated documentation, including on input selection and on custom germline presets (-g)
  • New and updated tests

Algo 2020-08-21⚓︎

  • Cleaned output, no .vdj.fa and seq/clone-*.fa by default, new options --out-vdjfa and --out-clone-files #4386 #4387 Pipelines should not rely on the format of the headers in the .vdj.fa file, but rather parse the .vidjil file #3795
  • Extended test and support to g++ 10.1, while reworking the documentation on supported compilers !733
  • Updated documentation
  • Updated the functional test framework (tools/should.py) !669 !784, new and updated tests

Algo 2020-06-12⚓︎

  • New report of 'start of V' and 'end of J' positions #2138, improving the productivity estimation #2142 This is based on a streamlined alignment for reverse sequences (core/segment.cpp) !706
  • Faster and improved probability computations (core/proba.cpp) !679 This will bring further speed-ups in a future release
  • Ctrl-C now gracefully stops execution with a warning W09 and some output #4286
  • Streamlined handling of warnings #3360, also reported with -c designations #3811
  • Better and more reproducible speed and memory benchmarks (benchmark-releases.py, #4275) #918, new profiling #918
  • Adoption of 'detected' term, renamed output files to '.detected.vdj.fa' #3413
  • Updated documentation
  • New and updated tests
  • Better release process through a merge request template !685

Algo 2020-05-02⚓︎

  • Bug closed (crash in very rare cases #4272)

Algo 2020-04-29⚓︎

  • New --gz option to output compressed files #4253 #4269 #4270
  • Improved seed framework, with different seeds on V/D/J parts. Analysis will be improved in further releases #3954
  • Bugs closed (missing affectations #4225, crash in rare cases #4263)
  • New Docker framework for tests on multiple compilers #4203
  • New and updated tests

Algo 2020-01-24⚓︎

  • Improved e-value estimation, -e is now the global e-value, new advanced option --e-value-kmer Sequences on larger datasets will now be better analyzed BF 3594 !538
  • Added 'seg.cdr3.seq' output with nucleotide sequence #4017
  • Improved 'name' output on sequences not fully analyzed with '-c designations' #3890
  • Limit on 50 clones on stdout, as the main output is the .vidjil file #3302 !530
  • New --no-vidjil and --no-airr advanced options to control the output #3861
  • Extended and updated documentation, including on library preparation and sequencing and on quality
  • New and updated tests

Algo 2019-05-17⚓︎

  • Better method to build consensus sequences used by default, old behaviour with --consensus-on-longest-sequences #3866
  • Optimized analyses with pre-computations, including for e-value estimation !468
  • Updated functional .should tests with new syntax, renaming and moving some tests #3206 #3762

Algo 2019-04-04⚓︎

  • New --config and --label-json experimental options (vidjil.cpp, lib/CLI11_json.cpp) #3837 #3839
  • Improved computation of consensus sequence when there are many reads (vidjil.cpp) !448
  • Better --alternative-genes reporting, including genes with same score (core/segment.cpp) #3414
  • Updated the functional test framework (tools/should.py)

Algo 2019-03-14⚓︎

  • New --consensus-on-random-sample experimental option (core/representative.cpp) #3764
  • Aho-Corasick automaton used by default (vidjil.cpp) #2566, will bring speed-ups in a future release
  • Refactored command and option names, deprecate some short options names (vidjil.cpp) #3295 #3772
  • Bug closed (incorrect deletion reported on unexpected recombinations, core/segment.cpp) BF 3518
  • Updated documentation
  • Improved test framework (tools/should.py), updating code coverage, test compilation warnings #1233
  • New and updated unit and functional tests

Algo 2018-11-26⚓︎

  • Corrected 2018-10 release, works now on all suported platforms #3601 #3062 (core/output.cpp)
  • Updated the functional test framework, relaunching some tests (tools/should.py)

Algo 2018-10-31⚓︎

  • New option --alternative-genes, outputs germline genes beyond the most probable one (core/segment.cpp) #1459
  • New warning W69 for equally probable germline genes (core/segment.cpp) #3575
  • Improved again memory usage, creating bins only when necessary (core/readstorage.cpp) #3393
  • Improved the full analysis pre-processing, extending -Z 1 based on probabilities (core/filter.cpp, core/math.cpp) #3225
  • Refactored output handling (core/output.cpp) #3858
  • New AIRR .tsv output (core/output.c) #2828
  • Updated documentation
  • New and updated unit and functional tests
  • Known regressions: This version may not work on some systems #3601 #3602

Algo 2018-07-18⚓︎

  • Cleaned memory after the heuristic, lowering memory usage up to 50% on datasets with many 1-read clones #2120 #3387

Algo 2018-07-16⚓︎

  • New default option -Z 3, speeding up the full analysis of clones with a pre-processing based on k-mers #3298 Processes with -c segment or with large -z values will be between 2x and 15x faster (vidjil.cpp, core/filter.cpp)
  • Integrated and extended up/downstream regions, improving analysis of heavily deleted 3' genes (germline/) #3008 #3009
  • Corrected the heuristic in borderline cases with overlapping VJ affectations (core/affectanalyser.cpp) #3296
  • Streamlined handling of seeds, enabling the use of aliases with -s (core/tools.cpp) #3293
  • Refactored option processing for vidjil-algo with CLI11 (lib/CLI11.hpp, vidjil.cpp) #2732
  • Improved build time up to 40% (lib/json_fwd.h) #3307
  • Updated third-party library (lib/json.hpp) #2935
  • Improved build and release process, supporting also g++ 7.3 and testing several compilers (.gitlab-ci.yml) #3002 #3015 #3310
  • Removed unused code and CI parts #3294 #3287
  • Updated documentation, converted into .md files (#3004)
  • Refactored and re-enabled code coverage, making it publicly accessible on Gitlab (algo/Makefile, .gitlab-ci.yml) #1696
  • New and updated unit and functional tests

Algo 2018-06-14⚓︎

  • New experimental option -Z to speed-up the full analysis with a pre-processing based on k-mers (core/filter.cpp) #920
  • New experimental analysis of Ikaros/ERG recombinations (germline/homo-sapiens-ikaros.g) BF 2139
  • Improved analysis with large number of mutations in V or J genes (core/dynprog.cpp) #3066
  • Added levels to warnings, lowering level for W53 (core/tools.cpp) #3136 #3137
  • Refactored the functional test framework (tools/should.py) #3105
  • New and updated unit and functional tests

Algo 2018-02-02⚓︎

  • Renamed program to 'vidjil-algo'
  • Improved analysis of large deletions in V or J genes (core/segment.cpp) #2767
  • Improved analysis of reads where V/J junction is close to an end, slightly shifting or shortening the window (core/segment.cpp, core/windowExtractor.cpp) #2913
  • Removed default homopolymer cost, improving detection on the majority of sequencers (core/dynprog.h) #2851
  • Added warnings in the json output on some clones #2916
  • Bug closed (clean some germinal sequences #2598)
  • Corrected memory leaks #3018 #3031
  • Cleaned folders, with sources in src/, demo data in demo/, test data in algo/tests/data/ #2635 #2611
  • Changed option processing library, trying CLI11 instead of docopt (lib/CLI11.hpp, tools/align.cpp) #926
  • Streamlined packaging and Makefile, based on git #2255 #2630
  • Updated build process (supporting g++ 4.8 to 7.2, clang from 3.3), warns on non-supported compilers #2614 #2615 #2631
  • Updated help and online help, added demo files and commands, -f option #2635 #2076
  • Refactored unit tests with TEST_TAP_EQUAL #2989
  • New and updated unit and functional tests, including tests from documentation #1284 #2634

Algo 2017-09-08⚓︎

  • New BAM input parser, refactored input parsers (core/bioreader.cpp, core/bam.cpp) #2016
  • Streamlined seed options (-m, -k, -s), overriding -g presets (vidjil.cpp, core/germlines.cpp) #1673 #2156
  • New and updated unit and functional tests #2016 #2552
  • Faster tests (tests/Makefile, tests/*) #2254
  • Bug closed (halting when a representative is too short) #2224
  • Documented dependencies and libraries (lib/info.txt)
  • Updated help, correcting -h documentation on -u/-uu/-uuu options
  • Moved continuous integration to Gitlab CI (.gitlab-ci.yml)

Algo 2017-03-14⚓︎

  • Better support for germlines from several species (germlines/*.g) #1987 #2132
  • Streamlined option -g, including filtering, removed old -i/-G options (vidjil.cpp, core/germline.cpp) #2134
  • Better productivity estimation, handling in-frame stop codons (core/segment.cpp) #2220
  • Better unsegmentation causes, 'UNSEG only V/J' needs really significant V/J fragments (core/segment.cpp) #2107
  • New experimental faster heuristic with Aho-Corasick automaton (core/automaton.hpp) #1366
  • New option to disable window clustering (-w all) (core/windowExtractor.cpp) #1642
  • Updated germline genes from IMGT/GENE-DB
  • Bugs closed (json output, consensus computation, -y option) #2214 #2217 #2224 #2239
  • Refactored test structure for should-vdj tests (tests/should-vdj-to-tap.py, tests/repseq_vdj.py)
  • New and updated unit and functional tests, including more solved former bugs
  • Moved code to gitlab, better project management, commit messages are now linked to issues

Algo 2016-09-30⚓︎

  • New default trim option (-t 0) for germlines, leading to better results on some special recombinations (vidjil.cpp)
  • More flexible option to keep sequences of intereset (-W), accepting sequences of any size (core/windows.cpp)
  • Better generation of consensus sequences, marking ambiguous positions with Ns (core/representative.cpp)
  • Better recognition of standard recombinations by lowering incomplete germline attractiveness (core/segment.cpp)
  • Better TRD locus analysis, including some Dd-Dd-Jd recombinations (data/germlines.data)
  • Reduced unused similarity section of .json file output (vidjil.cpp)
  • New json output with -c segment (vidjil.cpp)
  • Updated help (doc/algo.org)
  • New and updated unit and functional tests, updated test process

Algo 2016-08-06⚓︎

  • New computation of average quality for each representative sequence, inside its window (core/representative.cpp)
  • New option (-E) to set the e-value for FineSegmenter D segment detection (vidjil.cpp)
  • Safer e-value estimation for D segments (vidjil.cpp)
  • Raised capacity to 2*10^9 reads (core/segment.cpp, core/fasta.cpp)
  • Better filtering/debug options (-u/-uu/-uuu), keeping interesting reads (vidjil.cpp, core/windowExtractor.cpp)
  • Better .vdj.fa header for irregular/incomplete recombinations, 1-based positions (core/segment.cpp)
  • Bugs closed (-u files, similarity in .vidjil)
  • New and updated unit and functional tests, checking again .should-vdj tests

Algo 2016-07-13⚓︎

  • New json 2016b format, renamed fields 'seg.{5,4,3,evalue}' and 'diversity', 1-based positions (core/segment.cpp)
  • New tool to display and debug alignments between a read and selected V/J genes (tools/vdj_assign.cpp)
  • Better test structure and process. The should-vdj tests will be soon moved to their own repository.
  • Bugs closed (build process, affine gaps (core/dynprog.cpp), JUNCTION/CDR3 detection (core/segment.cpp))
  • New and updated functional tests

Algo 2016-03-04⚓︎

  • Better JUNCTION/CDR3 detection (-3), based on positions of Cys104 and Phe118/Trp118 (core/segment.cpp)
  • Bugs closed (.vidjil output of revcomp'd sequences, computation of Simpson index Ds)
  • Streamlined structure of tests directory
  • New and updated unit and functional tests

Algo 2016-02-08⚓︎

  • New default threshold (-z 100), fully analyzing more clones
  • New computation of diversity indices (Shannon, Simpson) (core/windows.cpp)
  • Streamlined KmerSegmenter test (core/affectanalyser.cpp)
  • Safer p-value estimation in KmerSegmenter, taking into account the central region (core/affectanalyser.cpp)
  • New experimental VDDJ detection analysis (-d) (core/segment.cpp)
  • Better FineSegmenter V(D)J designation for inverted genes in unexpected recombination analysis (core/segment.cpp) The unexpected recombination analysis (-2) can now safely be used.
  • Streamlined FineSegmenter handling of V, D and J segments (core/segment.cpp)
  • Faster FineSegmenter (~30%), relying on the KmerSegmenter to select to correct strand (core/segment.cpp)
  • Updated germline genes from IMGT/GENE-DB
  • Bugs closed (.vidjil output for sequences beyond the -z threshold)
  • New and updated unit and functional tests

Algo 2015-12-22⚓︎

  • Better KmerSegmenter, rejecting reads with large alterning V/J zones (core/segment.cpp)
  • Better unsegmentation causes, 'UNSEG only V/J' needs significant V/J fragments (core/segment.cpp)
  • Renamed unsegmentation messages to "only V/5'" and "only J/3'" to avoid confusion (core/segment.h)
  • Better unexpected recombination analysis (-2), with a FineSegmenter V(D)J assignation (core/segment.cpp)
  • Faster FineSegmenter (~35%), computing roughly half of the dynamic programming matrix (core/segment.cpp)
  • More flexible handling of badly formatted .fastq files (core/fasta.cpp)
  • New filtering/debug option (-uu), sort unsegmented reads (core/windowExtractor.cpp)
  • Streamlined json output, removing short codes (vidjil.cpp, core/segment.cpp)
  • Updated and refactored help (doc/algo.org)
  • Updated unit and functional tests
  • Bugs closed (build process, -X with large numbers, -x/-X combined with -c segment, stdout messages)

Algo 2015-10-08⚓︎

  • Bug closed (V(D)J assignation when V/D/J segments are close on the negative strand) (core/segment.cpp)

Algo 2015-10-05⚓︎

  • Better FineSegmenter V(D)J assignation, especially when V/D/J segments are close (core/segment.cpp)
  • Better e-value computation for FineSegmenter V(D)J assignation (core/segment.cpp)
  • Renamed 'UNSEG too few J/V' to 'UNSEG only V/J' to better reflect the actual detection of one part
  • Refactored tests for V(D)J assignation, allowing flexible patterns, new documentation (doc/should-vdj.org)
  • New tests on sequences with manually curated V(D)J assignations (tests/should-vdj-tests)
  • Bugs closed (no more spurious D in some VJ recombinations, corrected number of deletions around D regions)

Algo 2015-07-21⚓︎

  • New flexible parameterization of analyzed recombinations through a json file (germline/germlines.data)
  • New experimental unexpected recombination analysis (-4 -e 10) (core/segment.cpp)
  • New threshold for FineSegmenter VJ assignation, with at least 10 matches (core/germline.cpp)
  • Streamlined handling of segmentation methods (core/germline.h, core/segment.cpp)
  • Updated distance matrix computation between all clones (core/similarityMatrix.cpp)
  • New nlohmann json libray to parse and write json files (lib/json.h)
  • Updated build process, now requiring a C++11 compiler
  • New draft developer documentation (doc/dev.org), updated help and user documentation
  • New and updated unit and functional tests, bugs closed in shouldvdj tests

Algo 2015-06-05⚓︎

  • New default trim option (-t 100), considering only the relevant ends of the germline genes
  • Better segmentation heuristic when there are few k-mers (core/segment.cpp)
  • Better TRA/TRD locus analysis (-i), including both Vd-(Dd)-Ja and Dd-Ja recombinations (core/germline.cpp)
  • Better incomplete TRD and Dh/Jh analysis (-i), including up/downstream region of D genes (core/germline.cpp)
  • Better computation of the reference length for the coverage information, considering all reads of each clone
  • Better unexpected recombination analysis (-2), with information on the locus used (core/segment.cpp)
  • Streamlined again unsegmentation causes and removed delta_{min,max} for the heuristic (core/segment.cpp)
  • Refactored stats computation (core/read_storage.cpp)
  • Updated build process The next release will require a C++11 compiler. Static binaries will also be distributed.
  • Updated help (unsegmentation causes, clustering options, -m option)
  • Bugs closed (segmentation with k-mers on the negative strand, e-value computation, clone output on stdout)
  • New and updated unit and functional tests, and faster functional tests

Algo 2015-05-08⚓︎

  • New default e-value threshold (-e 1.0), improving the segmentation heuristic
  • New default for window length (-w 50), even with -D or with -g, streamlining the window handling
  • Better multi-germline analysis (-g), selecting the best locus on the e-value (core/segment.cpp)
  • New experimental trim option (-t), considering only the relevant ends of the germline genes (core/kmerstore.h)
  • Streamlined unsegmentation causes, including 'too short for w(indow)'
  • Updated main and debug ouptut
  • Updated help (algo.org, and new locus.org)
  • New option to keep only reads with labeled windows (-F), new combo (-FaW) to filter reads by window
  • Bugs closed (non symmetrical seeds and revcomp)
  • New and updated unit and functional tests

Algo 2015-04-09⚓︎

  • New experimental e-value threshold (-e) (core/segment.cpp)
  • New experimental unexpected recombination analysis (-2) (core/segment.cpp)
  • New preview/debug options to stop after a given number of reads (-x), possibly sampled throughout the file (-X)
  • New preview/debug option to output unsegmented reads as clones (-!)
  • New progress bar during computation
  • Better memory management for the reads taken into account for the representative (core/read_storage.cpp)
  • Updated .json output, with k-mer affectation results
  • Updated .json output, with the 'coverage' of the representative (core/representative.cpp)
  • Removed unused code parts as well as some files
  • Updated help, separing basic (-h) and advanced/experimental options (-H)
  • Bugs closed (extended nucleotides and revcomp)
  • New and updated unit and functional tests

Algo 2015-03-04⚓︎

  • Better multi-germline analysis (-g), returning the best locus for each read (core/segment.cpp) The incomplete rearrangement analysis (-i) can now safely be used. The speed of this multi-germline analysis will be improved in a next release.
  • Faster representative computation (core/read_chooser.cpp)
  • Included tools (tools/*.py) to process .vidjil files
  • New statistics on the number of clones (core/germline.cpp)
  • New experimental CDR3 detection (-3). We still advise to use IMGT/V-QUEST for better and complete results.
  • Better debug option -K (.affect), especially in the case of multi-germline analysis
  • Refactored dynamic programming computations (core/dynprog.cpp), experimental affine gaps
  • Removed unused code parts as well as some files
  • Streamlined flag processing in Makefiles
  • New mechanism for some functional tests (make shouldvdj)
  • New experimental tests from generated recombinations (make shouldvdj_generated)
  • New and updated unit and functional tests

Algo 2015-01-31⚓︎

  • Better TRG and TRD+ parameters (-g). The multi-germline analysis will again be improved in a next release.
  • New experimental option (-I) to discard common kmers between different germlines (core/germline.cpp)
  • Updated outputs for better traceability (version in .json, germlines on stdout)
  • New mechanism to retrieve germline databases (germline/get-saved-germline)

Algo 2014-12-22⚓︎

  • Better multi-germline analysis (-g). This will again be improved in a next release.
  • New experimental incomplete rearrangement analysis (-i)
  • New and updated unit and functional tests
  • Bugs closed (-w 40 when no D germline)

Algo 2014-11-28⚓︎

  • New input method, now accepts compressed fasta files with gzip (core/fasta.cpp, gzstream/zlib)
  • Better multi-germline analysis (-g) and documentation. This analysis can now safely be used.
  • Streamlined input. Option -d is removed, and a germline is required (-V/(-D)/-J, or -G, or -g)
  • Removed unused code parts as well as some files
  • New and updated unit and functional tests - now more than 80% code coverage
  • New public continuous integration - travis, coveralls
  • Bugs closed (-l, large -r)

Algo 2014-10-22⚓︎

  • Streamlined filtering options (-r/-y/-z), better documented (doc/algo.org)
  • Streamlined output files, option to fix their basename (-b)
  • Updated .data .json output, now in the better documented 2014.10 format (doc/format-analysis.org)
  • New experimental multi-germline analysis (-g). This will be improved and documented in a next release.
  • Faster FineSegmenter with a better memory allocation (core/dynprog.cpp)
  • Refactored main vidjil.cpp, objects storing germlines and statistics (core/germline.cpp, core/stats.cpp)
  • Transferred clustering from clone output to information in .data, again simplifying vidjil.cpp
  • Removed unused code parts as well as some files
  • New and updated unit and functional tests
  • Bugs closed

Algo 2014-09-23⚓︎

  • Export cause of non-segmentation in the .data
  • New option to output segmented reads (-U), now by default segmented reads are not output one by one
  • Updated .data .json output (the format will change again in a next release)
  • Updated tests

Algo 2014-07-28⚓︎

  • Better heuristic, segment more reads (core/affectanalyser.h, core/segment.cpp) This improved heuristic was designed to implement a multi-germline analysis in a next release.
  • Improved computation of the heuristic affectation. Halves the time of -c windows (core/kmerstore.h)
  • New command '-c germlines', discovering germlines (vidjil.cpp)
  • New unit tests, updated some tests
  • Updated .json output (experimental distance graph)
  • Bugs closed

Algo 2014-03-27⚓︎

  • Better default seed selection, depending on the germline, segments more reads (vidjil.cpp)
  • Better selection of representative read (core/representative.cpp)
  • New option to output all clones (-A), for testing purposes
  • Updated debug option (-u) to display k-mer affection (core/windowExtractor.cpp)
  • New unit tests, updated some tests
  • Improved management of dependencies (Makefile)
  • Improved documentation and comments on main stdout

Algo 2014-02-20⚓︎

  • Refactored main vidjil.cpp (core/windows.cpp, core/windowExtractor.cpp)
  • Removed unused html output
  • Better json output (core/json.cpp)
  • Updated main stdout, with representative sequence for each clone
  • Updated parameters for FineSegmenter (delta_max) and dynprog (substition cost)
  • Bugs closed

Algo 2013-10-07⚓︎

  • Better heuristic, segments more reads (core/segment.cpp)
  • Better and faster selection of representative read (vidjil.cpp, core/read_chooser.cpp)
  • Better display of reason of non-segmenting reads
  • New normalization against a standard (-Z) (core/labels.cpp)
  • New experimental lazy_msa multiple aligner
  • New .json output
  • New unit tests
  • Bugs closed

Algo 2013-07-03⚓︎

  • New selection of representative read (core/read_chooser.cpp)
  • Faster spaced seed computation (core/tools.cpp)
  • New unit tests
  • Bugs closed

Algo 2013-04-18⚓︎

  • First public release