versions: 1st numeric part = milestone releases; 2nd = major changes, mostly affecting results; 3rd = minor changes

1.99.8 | 19.09.22

• New capture deduplication mode for R and SV (QC and VAR keep the genome-alignment-based one).
• Fixes for iNext v3 (diversities).

1.99.7 | 31.08.22

• Docker dependencies.

1.99.6 | 29.08.22

• cfDNA pipeline scenario (ARResT.cfDNA - see 'cfDNA-Based NGS IG Analysis in Lymphoma' by C Pott et al, Immunogenetics 2022) enabled for ARResT-group users.
• Fixes and improvements.

1.99.5 | 12.07.22

• Oncoplot: enabled table filter to affect plot, full sample list always shown, Rs filter optional and corrected.

1.99.4 | 08.07.22

• Fixed bug in setting VAF thresholds in mutants module, plus minor improvements.
• Oncoplot panel.

1.99.3 | 01.07.22

• Fixes and improvements.

1.99.2 | 22.06.22

• Fixes and improvements.

1.99.1 | 22.06.22

• Traced clone selection error fixed.

1.99.0 | 02.05.22

• Improvements and fixes in 'middle' D gene identification.

1.98.3 | 29.04.22

• Fix for access to scenario primers and tracers, has been affecting non-EC-NGS accounts trying to use EC-NGS/EuroMRD scenarios.
• Fixes and improvements.

1.98.2 | 27.03.22

• Forensics table fix.
• WholeMark fixes.

1.98.1 | 01.03.22

• Trial integration.
• WholeMark user mode improvements.

1.98.0 | 28.02.22

• Improvements and fixes in 'middle' D gene identification (with more to come, incl. for IGH VDDJ and DDJ).

1.97.1 | 03.02.22

• Fixes and improvements.

1.97.0 | 13.01.22

• VJ:Va-Jd is now VJ:Va-(Dd)-Jd.
• Fixes and improvements.

1.96.5 | 07.12.21

• Trial integration and cleanup.
• Marksman reactivity.

1.96.4 | 02.12.21

• Marksman loading.
• Marksman - Cell view reactivity.

1.96.3 | 01.12.21

• TRIAL fixes.
• Minor fixes and improvements.

1.96.2 | 28.11.21

• Browser loading speed-up.
• Marksman panel available for testing.
• TRIAL-only WMD mode.
• Minor fixes and improvements.

1.96.1 | 05.11.21

• Minor fixes and improvements.

1.96.0 | 28.10.21

• Gene functionality is now taken into account towards productivity.
• TRIAL updates, incl. handling pooled samples.
• Marksman can now do molecular interpretation.

1.95.0 | 03.10.21

• Longer sequence storage, RSS filter permanently turned on, downstream J safeguard, capture tweaks, colab implementations.

1.94.1 | 29.09.21

• Minor fixes and improvements.

1.94.0 | 22.09.21

• Spike-in sweeping and pre-sweeped spike-in and artefacts update; better and safer capture contig assembly; TRIAL integration; 'gather' upgrade; fixes (incl. a crashing bug in the browser) and improvements.

1.93.000 | 08.09.21

• Further optimisation, routine parallelisation, capture mode update, improvements and fixes.

1.92.000 | 17.08.21

• More improvements/fixes/optimisations/clean-up for big data and generally.

1.91.001 | 09.08.21

• Big data mode improvements and fixes.

1.91.000 | 03.08.21

• Updated tracers, routine script parallelisation and usability, improvements and fixes.

1.90.012 | 23.07.21

• Improvements and fixes.

1.90.011 | 12.07.21

• Capture mode wrap-up, routine script optimisations.

1.90.010 | 30.06.21

• Capture mode work.

1.90.009 | 24.06.21

• Browser user modes and functionalities for capture mode, minor improvements and fixes.

1.90.008 | 20.06.21

• Capture mode and routine script work, WMD queuing, Roundup fix, TRIAL development, other minor improvements and fixes.

1.90.007 | 07.06.21

• Capture mode and routine script work, WMD legacy fix, TRIAL development, other minor improvements and fixes.

1.90.006 | 26.05.21

• Capture mode and routine script work, WMD reporting fix, other minor improvements and fixes.

1.90.005 | 19.05.21

• Improvements and fixes, for setting WMD cores and in capture-mode scenarios and inputs.

1.90.004 | 17.05.21

• Capture mode, incl.: better choice of sequences for rearrangement contig assembly + enabled artefact filtering, VEP update, translocation clonotypes, etc.
• Improvements and fixes.

1.90.003 | 13.05.21

• NOTICE - pre-v2 release: this version already has code, soon to be enabled as v2, that will affect junction aa sequences and clonotypes (for the better), see next points for some pointers - you can already ask us to enable it for you via pipeline scenarios.
• pre-v2 - junction nt sequence clustering is now more adapted to junction structure and even different receptors, being more specific and sensitive at the same time
• pre-v2 - junction aa sequences will now be virtually-in-frame (with #s) even if 2nd anchor is missing
• pre-v2 - in clonotypes, multiple equal 5' gene assignments will now be converted to '~[gene group]' if >=3 (before it was >=4)
• Memory optimisations, should be able to handle more millions of reads more easily (but will still be relatively slow).
• Numerous improvements and fixes.

1.23.000 | 10.02.21

• -- internal release --

1.22.000 | 22.10.20

• -- internal release --

1.21.340 | 30.07.20

• Accommodating PacBio base quality values.
• Improved sample filename handling (but for now avoid having FASTQ and FASTA with exactly the same name prefix if you don't specifically choose one to run).
• Improved primer files handling.

1.21.339 | 21.07.20

• Improvements and fixes, in pipeline reporting, and in EC-NGS primer set auto-detection (see 1.21.338) resulting in benign primer ALARMs not being silenced for IGH-VJ-FR1.

1.21.338 | 13.07.20

• Improvements and fixes, incl. in EC-NGS primer set auto-detection (see 1.21.335).

1.21.337 | 01.07.20

• Benign 'run name'-based bug fixed.

1.21.335 | 30.06.20

• We now allow hyphens in EC-NGS primer set auto-detection - in general, use these primer set names bookended by _ (or - or nothing at either end): IGH-VJ, IGH-VJ-FR[123], IGH-DJ, IGK-VJ-Kde, intron-Kde, IGK, TRB-VJ, TRB-DJ, TRG, TRD

1.21.334 | 24.06.20

• Run report fixes for capture mode.

1.21.333 | 03.06.20

• Improvements and fixes.

1.21.313 | 28.05.20

• Capture mode improvements and fixes, incl. a broken line affecting the 'mutants' module.

1.21.300 | 26.05.20

• New 'HQ' panel.
• Special capture mode speedup.
• Improvements and fixes.

1.21.257 | 07.05.20

• Improvements and fixes.

1.21.253 | 23.04.20

• Improvements and fixes.

1.21.252 | 20.04.20

• Improvements and fixes.

1.21.250 | 14.04.20

• Improvements and fixes.

1.21.204 | 02.04.20

• EuroClonality-NGS-specific work.
• Improvements and fixes.

1.21.166 | 25.03.20

• More work on artefacts, including automatic mode and pre-filtering.
• Improvements and fixes.

1.21.100 | 23.03.20

• Introduced 'artefacts', problematic but junction-like sequences provided by the user and identified, excluded and reported by the pipeline.
• Improvements and fixes.

1.21.000 | 03.03.20

• Major version bump since clonotyping MIGHT result in different results due to junctioning changes since 1.20.500
• Fixed issue, since 1.20.600, with virtual in-frame in special cases, i.e. when #s were initially placed inside D segment if P3nt>0 and N2nt=0 (=rare).
• Improvements and fixes.

1.20.699 | 11.02.20

• Improvements and fixes.

1.20.622 | 22.01.20

• Improvements and fixes.

1.20.620 | 20.01.20

• Improvements and fixes.

1.20.600 | 13.01.20

• Changed capitalisation of segmented junction sequences, i.e. 5' and 3' segments are now lowercase like a D segment was, which improves consistency (i.e. all germline segments are now lowercase) - N regions are still uppercase. Note that unsegmented junctions within full sequences are still all uppercase.
• EuroClonality-NGS-specific work.

1.20.520 | 07.01.20

• Many additions, improvements (incl. speedup) and fixes.

1.20.500 | 18.12.19

• Pipeline: D gene junction segmentation now provided by default inside junction nt sequence.
• Pipeline: more efficient clonotype clustering.
• Pipeline: clearer log output for 'no primer, no use' / 'no-primer' junctions.
• Pipeline: test for unsafe filename characters.
• EuroClonality-NGS-specific work.

1.20.422 | 22.11.19

• Added 'popjuclass' to capture clonotype definition.
• Improvements and fixes.

1.20.400 | 18.11.19

• Pipeline: improved reporting on primers, postmortem, capture.

1.20.313 | 13.11.19

• Minor improvements and fixes.

1.20.311 | 01.11.19

• EuroClonality-NGS-specific work.
• Pipeline: primers are now never trimmed from primerdimers to keep them informative.

1.20.300 | 15.10.19

• EuroClonality-NGS-specific work.

1.20.253 | 19.09.19

• EuroClonality-NGS-special user mode improvements and bug fixes.

1.20.250 | 03.09.19

• EuroClonality-NGS-specific work.
• Update for IMGT/V-QUEST 3.5.8.
• Minor improvements and fixes.

1.20.222 | 26.08.19

• Browser: completely removing pre-set primers and/or tracers from pipeline scenarios would not really work.
• Lots of EuroClonality-NGS-specific work, incl. on clonality reporting.
• Minor improvements and fixes.

1.20.202 | 09.08.19

• Pipeline: fixed the cursed per-primer set QC, again (issue in primer sets metadata, and number reporting).
• Pipeline: better handling of primer/tracer sequence files prepared in Windows.

1.20.200 | 08.08.19

• Pipeline: if EuroClonality-NGS primers are used but sample is not assigned to a single primer set, we consider it 'pooled', which activates per-primer set QC. Assign a primer set through the filename by enclosing the primer set in underscores, e.g. mysample-1_IGH-VJ-FR1_S99, or through a samplesheet and a 'primer set' column.
• Pipeline: fixed rare sample skipping during results gathering.
• Work on EuroClonality-NGS-specific code.
• Minor improvements and fixes.

1.20.100 | 25.07.19

• Pipeline: per-primer set QC info for pooled samples was still not OK, now OK.
• Minor improvements and fixes.

1.20.000 | 22.07.19

• Browser: new reporting panel for EC-NGS clonality user mode.
• Pipeline: increased distance between primers to call a primerdimer, now 18nt.
• Pipeline: per-primer set QC info for pooled samples introduced in previous major update was inadvertently disabled, now OK.
• Pipeline: fixed bug in run reports that would skip some per-feature-type stats, e.g. DJ:Dh-Jh stats.
• Pipeline: fixed bug (introduced in 1.19 and only seen in one public run) affecting the gathering of pipeline result parts.
• Minor improvements and fixes.

1.19.000 | 24.06.19

• Pipeline: improved logic for highly trimmed IGH incomplete rearrangements i.e. still safe while more sensitive.
• Pipeline: per-primer set QC info for pooled samples.
• Pipeline: more info on spike-ins in run and sample reports.
• Browser: improved tooltips and popups.
• Opened up 'EC-NGS' (EuroClonality-NGS) user modes (top-left corner) for more users, for processing data from EuroClonality-NGS SOPs for marker identification and clonality assessment (euroclonality.org/protocols/).
• Minor improvements and fixes.

1.18.500 | 30.05.19

• Pipeline: update for IMGT/V-QUEST 3.5.0 and its new API.

1.18.400 | 10.04.19

• Pipeline: FASTQ filtering now keeps zero-length reads to not break paired-end files.
• Browser: fix in V-QUEST test output formatting.

1.18.300 | 31.03.19

• Pipeline: improved stability.

1.18.100 | 25.02.19

• Pipeline: new feline germlines from our collaborator Stefan Keller.

1.18.003 | 12.02.19

• Pipeline: improved handling of missing/wrong primers, also in relation to downstream analysis.
• Pipeline: improved handling of .set primer files.

1.18.002 | 12.02.19

• QC finetuning.

1.18.001 | 06.02.19

• Minor improvements and fixes.

1.18.000 | 03.02.19

• Major speedup in tracing, and finetuning of tracing parameters.
• Multiple improvements and fixes, but mostly on internal functionalities not yet widely available (e.g. capture data).

1.17.800 | 09.01.19

• -- internal release --

1.17.700 | 07.01.19

• -- internal release --

1.17.500 | 20.12.18

• -- internal release --

1.17.000 | 09.12.18

• Pipeline: improved calling of rearrangements highly trimmed in both 5' and 3'.
• Pipeline: fixed the lack of junction segmentation is rare cases (junction and clonotype were still reported).
• Minor improvements and fixes.

1.16.500 | 03.12.18

• Pipeline/Browser.forensics: absent NDN region would show as '0' in forensics analysis.
• Pipeline: "spikesQC": 'loosened' code for ">=1 spike w 0rds" (now checked for top-tier spike-ins only) and "norm factor >1" (disabled) - will finetune further in the near future.
• Pipeline: improvements and fixes in 'trace evidence'.
• Pipeline: improved capture mode, incl. translocations.
• Pipeline: enabled soft-linking of input files, enabling better data management.
• Browser: disabled/tweaked functionalities that were problematic in some use cases, user notified accordingly.
• Minor improvements and fixes.

1.16.000 | 21.11.18

• Pipeline: improvements and fixes.
• Pipeline: improved capture mode, incl. translocations.
• Browser: alert banners implemented.
• Tweaks in email reports, also related to the existence of 'previous', 'stable', 'latest' version of Interrogate.

1.15.000 | 15.11.18

• -- 15.11.18 --
• Pipeline: segmentation stats were missing the zero for deletions.
• Email report now includes app version (previous/stable/latest).
• Browser.processing: fix for user-created scenarios.
• Minor improvements and fixes.
• -- 13.11.18 --
• Pipeline: segmentation stats now always have zero, with '-' prefix for deletions.
• Pipeline: removed shorthand productivity tag from default clonotype definition.
• Browser.processing: user-created scenarios renabled and editable.
• Minor improvements and fixes.

1.14.000 | 07.11.18

• Pipeline: identification of one additional D in more (esp. incomplete) junction classes.
• Browser.questions: minitable now has more info on its header, mainly sum of abundances, but also unique counts and rearrangement types when clonotypes are selected.
• Browser.forensics.network: major redesign / simplification of the UI, improvements and fixes, with more to come.
• Browser.forensics.tests: enabled ARResT/AssignSubsets (only relevant for CLL), improvements and fixes, incl. better handling of more sequences than we allow for some tests.
• Minor improvements and fixes.

1.13.200 | 16.10.18

• Minor improvements and fixes.

1.13.100 | 01.10.18

• Pipeline: work on capture and routine modes.

1.13.000 | 22.09.18

• Pipeline: improved capture mode, incl. slight improvement in junctioning sensitivity.
• Browser.user modes: work on using metadata as feature types.

1.12.000 | 14.09.18

• Pipeline: improved capture mode.
• Browser.forensics: 'network' alignments re-enabled, other improvements.

1.11.100 | 27.08.18

• Pipeline: improved/generalised annotation tracing.

1.11.000 | 21.08.18

• Pipeline: increased junctioning sensitivity.
• Pipeline: improved primer trimming and paired-end joining, esp. for amplicons fully contained in paired-end reads.
• Browser.forensics: DNJ-stem fix, was presenting more DN sequence than planned - DNJ-stems in 'questions' were OK.
• Added 'amplicon length' as a feature type when primers are used.
• Minor improvements and fixes.

1.07.900 | 30.07.18

• Browser.processing: fixed bug crashing pipeline scenarios with primers.

1.07.800 | 25.07.18

• Browser.questions: improved reporting of problematic adding/updating of metadata.

1.07.700 | 03.07.18

• Browser: uploading of samples with spaces in filename fixed.
• Browser: ordering of "clicked minitable" unified with tables in 'forensics' panel.

1.07.600 | 05.06.18

• Pipeline: better handling of gzipped files without .gz extension.
• Pipeline: better handling of samplesheet filenames.
• Browser: minitable abundance column now responds to options like absolute/relative.
• Minor improvements and fixes.

1.07.500 | 29.05.18

• Pipeline: more robust temporary file handling to avoid 'collisions'.
• Pipeline: finetuning the EuroClonality-NGS primer extension list for relevant scenarios, results might change, esp. for 'noisy' data.
• Browser: 'junction nt length' in bar plots now also numerically sorted and 0-count lengths filled-in by default, just like 'junction aa length'.
• Minor improvements and fixes.

1.07.000 | 27.05.18

• Pipeline: reject noisy J 5' alignments.
• Pipeline: slightly more sensitive D alignment.
• Minor improvements and fixes.

1.06.000 | 23.05.18

• Pipeline: ability to reattach a trimmed 3' primer if it's needed for annotation and junctioning = no need to keep all 3' primers on by default = alleviate effect of mis/priming on annotation.
• Pipeline: IMGT orphons are now excluded, as per IMGT/V-QUEST default.
• Pipeline: further optimisations towards speed and memory efficiency.
• Minor improvements and fixes.

1.05.100 | 21.05.18

• Browser: the 'minitable' is now ordered with 1st clicked on top, and the order is preserved into 'forensics' - it also includes a clicked counter to assist with tracking.

1.05.000 | 16.05.18

• Pipeline: RSS-based protection against unrearranged J segments taking over the actually rearranged J - mostly relevant for capture data.
• Pipeline: fatally-3'-trimmed rearrangements, on which we artificially append Ns at the end, now only have one such N (vs as many as probably missing according to coordinates) = less Xs in junctions, more (naturally) out-of-frame junctions, overall cleaner and more homogenious results.
• Minor improvements and fixes.

1.04.100 | 14.05.18

• Pipeline: actively handling non-unique read labels (we were exiting before) - still not healthy, so still an ALARM.
• Pipeline: when *all* samples have failed, we were still trying to 'gather evidence', now fixed.
• Browser: even better handling of samplesheets (e.g. when rows have metadata but no sample name) - still WIP.
• Browser: minor bug fixes in 'file' (column sorting in run report) and 'questions' (zeros when transposed) tables.

1.04.000 | 11.05.18

• Pipeline: improvements and fixes for chimeric alignments and DNJ-stems, even better false positive filtering.
• Browser: better handling of samplesheets (e.g. when rows have metadata but no sample name).

1.03.000 | 10.05.18

• Pipeline: better avoiding false positive junctions (special cases).
• Browser.questions: silly code update error on Tuesday evening, causing some plots to be disabled until Wednesday evening (the default tab, 'table', was OK).

1.02.000 | 09.05.18

• Pipeline: explicitly filtering out clearly false positive junctions (special cases).
• Browser.forensics: further improved ARResT/Interrogate output, incl. separate clonotype-based and D-based segmentations and better tooltips.

1.01.100 | 08.05.18

• Pipeline: major speedup, up to 33% faster for big data, with more to come.
• Browser.forensics: improved ARResT/Interrogate output, with more compact with tooltips and colours.
• Minor improvements and fixes.

1.01.000 | 07.05.18

• Pipeline: major speedup, up to 33% faster for big data, with more to come.
• Pipeline: further work on D-REGION annotation of complete rearrangements, including deletions and segmentation representation - available in 'forensics', WIP.
• Minor improvements and fixes.

1.00.000 | 30.04.18

• .xlsx files can now be used across Interrogate, plus many improvements and bug fixes in their use (but also WIP).
• Browser.forensics: more tests, incl. for clonal evolution.
• Pipeline: less/smarter ALARMs.
• Pipeline: work on D-REGION annotation of complete rearrangements, including deletions and segmentation representation - available in 'forensics', WIP.
• Pipeline: improvement in annotation of D-based incomplete rearrangements, with more weight on D-REGION vs UTR/RSS, which e.g. better avoids 'noise' from mispriming.
• Pipeline: more natural gene and allele sorting.
• Pipeline: IMGT germlines update from 201728-2 to 201814-3.
• Minor improvements and fixes.

0.30.400 | 18.04.18

• EuroClonality-NGS work, esp. quality control.
• Minor improvements and fixes.

0.30.300 | 08.04.18

• EuroClonality-NGS work, esp. marker screening - expect/look for changes in user modes, scenarios, primer sets, underlying calculations.
• Browser.file: made sample name matching more flexible for updating metadata, i.e./e.g. incoming sample names can be shorter than existing.
• Minor improvements and fixes.

0.30.200 | 26.03.18

• Minor improvements and fixes.

0.30.100 | 21.03.18

• Browser: default analysis pre-selected in 'processing', you can now directly upload samples.
• Browser: user interface tweaks.
• Pipeline: fixed sample sorting in results.
• Implementation improvements for sample DNA copies and spike-ins.
• Minor improvements and fixes.

0.30.000 | 27.02.18

• Browser: major simplification of the user interface, and numerous improvements and fixes.
• Browser: revived/improved user messaging, the black bar under the panels, providing info and advice based on user actions.
• Browser.questions: clonotypes are now the default feature type.
• Browser.questions: feature-sample heatmap now resembles the main table by default (both can be transposed).
• Browser.file: Interrogate results filesizes now available in the drop-down list.
• Browser.file: you can update the results list with a button next to the drop-down.
• Browser.forensics: 'tests' has been updated, and now includes ARResT/Interrogate itself (i.e. the pipeline), and ARResT/AssignSubsets for the major stereotyped subsets in CLL.
• Pipeline: gene functionality, according to IMGT, is now used to choose from multiple options, e.g. prioritise F over ()/[]/P/ORFs.
• Pipeline: improvements in logs and reports.
• Pipeline: improvements in primer and primerdimer detection and analysis.
• Pipeline: improvements in rearrangement segmentation analysis, esp. with indels, and for DJ incomplete.
• More diversity calculations in the run report, based on all clonotypes - use with care though, e.g. when comparing between samples esp. of differing depth.

0.29.000 | 18.01.18

• -- internal release, see newer version --

0.28.000 | 08.01.18

• -- internal release, see newer version --

0.27.000 | 29.12.17

• -- internal release, see newer version --

0.26.001 | 06.12.17

• Browser: sorting features in heatmap like in barplot.
• Browser: spike-in normalisation table improvements.
• Browser: spike-in normalisation disabled, when no cell number info.
• Browser: top N features filtering fixed.
• Browser: demo file fixed.

0.26.000 | 01.12.17

• Pipeline: publicly introduced the term 'usable', for reads that will be used for relative abundances - this is a layer above 'with junction', e.g. spike-ins are with junction but are excluded from abundance calculations.
• Pipeline: mitigated the effect of mis-priming on (mainly) 'DJ:Dh-Jh' rearrangements - more homogenised annotations.
• Pipeline: using 5' gene groups in clonotypes instead of >=3 (optional and user-settable) multi-gene '=' assignments, e.g. 'VJ:Vh-(Dh)-Jh V3-11=V3-21=V3-48=V3-69-1=V3-7 1/26/2 J4 CARVSIQDDSSRYFDYW pro' to 'VJ:Vh-(Dh)-Jh ~V3 1/26/2 J4 CARVSIQDDSSRYFDYW pro' - note the "~".
• Minor improvements and fixes.

0.25.001 | 29.10.17

• Browser: hiding of scrollbars in table's fixed columns in Chrome and IE 10+.
• Browser.UI: improvements and minor bug fixes.
• Browser: improvements & fixes for CLLpedia user mode.

0.25.000 | 19.10.17

• Browser: hiding of inside-cell scrollbars in 'table' in Chrome and IE 10+.
• Extra info printed in run report, incl. numbers of unique sequences and clonotypes, and clonotypes per junction class.
• Pipeline: increased 'sensitivity' in trying to correct junction gene offsets and deletions, i.e. applying to sequences of lower abundance - more homogenised results.
• Pipeline: primer info is now used to dereplicate single-end reads, i.e. IonTorrent - lighter, faster, better.
• Pipeline: fixed annotation issues with reverse orientation sequences, i.e. IonTorrent.

0.24.100 | 17.10.17

• Browser: fixes and major speedups in sequence retrieval, esp. for popular features.
• Browser: fixed heatmap .html downloading.
• Pipeline: improvements and tweaks in trace_evidence with anno-tracing (WIP).

0.24.004 | 03.10.17

• Browser: fixed .xls format downloading.
• Browser: heatmap .html downloading temporarily disabled.

0.24.003 | 01.10.17

• Pipeline: faster file/sample testing, with improved reporting.
• Pipeline: fixes in email reporting for failed runs.

0.24.002 | 29.09.17

• Server: idle timeout increased, improving stability.
• Browser: overview tab stability and speed improvements.
• Browser: bar plot optimizations.

0.24.001 | 27.09.17

• Browser: stability improvements.
• Browser: minor fixes of reordering and renaming samples.

0.24.000 | 25.09.17

• Browser: the update to R 3.4+ caused some speed and stability issues, which should be resolved now - please provide feedback if you face trouble.
• Browser: upload size limit, which might have affected some users/analyses, increased to 100GB per upload 'event' - tip: if files get corrupted, try re-uploading them.
• Browser: normalised sample diversity is now used.
• Browser: functionalities for junction class sets (mainly used for filtering and abundance normalisation) improved.
• Browser.forensics: revived sequence analysis button in network tab.
• Browser.statistics: improved, incl. printing diversity numbers instead of only plotting them.
• Browser.questions: fixed ordering of samples from the samples selecting widget.
• Browser.questions: "rename samples to" was hiding data in visualisations.
• Browser.questions: the "most abundant features {A} to plot" was misbehaving for >50 features to plot, i.e. working in reverse.
• Browser.processing: updated scenario options and descriptions.
• Browser.processing: the run output is now more complete, and sticks around until next run.
• Pipeline: better output from WMD.
• Pipeline: more sensitive primer trimming.
• Pipeline: during dereplication, the most popular primer tags are now selected per uniread (TIP: extend with primers if you need more more high-res primer counts).
• Pipeline: order of magnitude speedup of sequence storage.
• Pipeline: non-segmentable junctions in clonotypes are now indicated with "\\" instead of with "x/x/x".
• Pipeline: FASTA files are now used better, e.g. with primers.
• Pipeline: quality trimming on both 5' and 3' if no primers used - USE PRIMERS!
• Pipeline: improved file/name handling.
• Pipeline: impoved ALARM messages and hints n' tips.
• Pipeline: detected primerdimers are now not even tried for junctions - cleaner, faster.
• Pipeline: calculating and reporting abundance of most pop clonotype, and normalised sample diversity.
• Pipeline: option to trim final annotated sequence in different ways (leave as is, annotated only, etc).
• Pipeline: development work on the capture and break_in (=translocations) modules.
• Pipeline: (ongoing) development work on fast-tracing and auto-tracing (incl. the ability to normalise per junction class sets).
• Improvements and bug fixes all around.

0.23.101 | 01.08.17

• Pipeline: improved 'low priming due to long amplicons' ALARM.
• Pipeline: improved code checks to avoid STDERRs in junctioning.

0.23.100 | 31.07.17

• Browser.questions/forensics: retrieving sequences for clicked samples/features improved (now always based on both feature types).

0.23.000 | 28.07.17

• Browser.UI: improvements and minor bug fixes (e.g. 'file': upload of metadata re-ordered samples but not the metadata themselves).
• Pipeline: improved sensitivity for D-based incomplete rearrangements.
• Pipeline: major memory and speed optimisations.
• Pipeline: updated trace and fast_trace code and functionalities, incl. new fast_trace options and values.
• Pipeline: fixed a bug when re-trying to annotate 3' ends, which if applicable resulted in decreased junctioning.
• Pipeline: nt junction clustering (also used for defining clonotypes) would sometimes assign very-low-abundant junctions to confusing, but not really incorrect, clusters - now this is is more robust, and might become even more flexible in the future.
• Pipeline: facility to trim on quality, esp. if no primers were used - still under development though.
• Pipeline: more informative messaging in case of trouble.
• Pipeline: better reporting, e.g. redundant/out-of-context ALARMs.
• Pipeline: other improvements and minor bug fixes.

0.22.100 | 15.06.17

• Browser.visualisations: fixed "most abundant features to plot" widget, which had a reversed logic for a little while.
• Browser.questions: fixed junction-class-based normalisation.
• Browser.questions: renamed several widgets and messages to improve usability, e.g. "select/filter on" buttons -> "show".
• Browser.processing: improved stability of the user files tab.
• Pipeline: improved handling of (very) long filenames.

0.22.000 | 15.05.17

• -- list created 03.05.17, updated 15.05.17, version kept since pipeline not released --
• -- 15.05.17 --
• Pipeline: alignment edge refinement, better NDN definition.
• Pipeline: more consistent handling of mutation/indel corrections across junction classes.
• Pipeline: 'process' module optimisation.
• Pipeline: improvements and minor bug fixes.
• Browser.heatmaps: improve slider range / step.
• Browser.forensics: bug fixes due to introduction of junction segmentation.
• Browser.questions: bug fixes in visualisations.
• -- 03.05.17 --
• Pipeline: junction segmentation, numerical NDN and functionality code in clonotype definition.
• Pipeline: 5' D and 'middle' D are now put together as 5' with '&' separator.
• Pipeline: updated to latest IMGT germlines (201715-4).
• Browser.UI: improvements incl. major speed-ups for visualisations, simplifications (in '.simple' user mode), and bug fixes all around.
• Browser.UI: new '.clones' user mode, with auto-select after data load, and clonotypes heatmap as default view.
• Browser.UI: some real-time widgets now respond with some delay to improve performance for big data.
• Browser.questions: 'clicked'-feature table now provides full segmented nt seq when appl.
• Browser.questions: moved 'clicked'-feature table on top of all widgets.
• Browser.questions: sorted-by-abundance bars and heatmaps now go from left (min) to right (max) (was other way before).
• Browser.heatmaps: new functionalities and major improvements, with more to come.
• Browser.heatmaps: swapped clustered sample-feature heatmap axis to match regular sample-feature heatmap.
• Browser.file: improved colouring of of run report table.

0.22.000b | 19.04.17

• -- pre-release --

0.21.100b | 13.04.17

• -- pre-release --
• Browser.heatmaps: new functionalities and major improvements, with more to come.
• Browser.UI: improvements and bug fixes all around.
• Browser.forensics: fixed recent bug introduced in previous update that compromised retrieved sequences.

0.21.000b | 07.04.17

• -- pre-release --
• Restored spike-in fast-tracing and functionalities in pipeline and browser.
• Browser.forensics: output improvements in sequence analysis.
• Pipeline: fixed/improved handling of gzipped mutli-lane samples in process.
• Pipeline: improved virtual-in-frame for junctions with 3' D.
• Pipeline: functionality and functionality comments expanded for 5' and 3' regions, improved for nonVJ junction classes.

0.20.510 | 26.03.17

• Browser.questions: improved presentation of (pre-)filtered data.
• Pipeline: updated dragnet descriptions.

0.20.500 | 22.03.17

• Browser.questions: (pre-)filtered features and feature combos now shown by default, plus major improvements of their presentation in visualisations.
• Browser.questions: NEW 'feature vs. feature heatmap' after clicking on a single cell in sample vs. sample distance heatmap.
• Browser.questions: minor improvements and bug fixes.
• Pipeline: dragnet technical pre-filtering now also 'protects' primers, on top of (currently) genes, junction lengths, and tracers.
• Pipeline: improved alarm and log messages.
• Pipeline: smarter file vs. sample names handling, improved reporting.
• Pipeline: DD:Db-Db junction class-related safeguard.
• Pipeline: improvements in the capture module.

0.20.100 | 08.03.17

• Browser.forensics: improved IMGT output formatting.
• Pipeline: improved log messages, e.g. for primer dimers, incl bug fixes, e.g. Q in run report.
• Pipeline: improved R1/R2 handling.
• Minor fixes and improvements all around.

0.20.000 | 06.03.17

• Browser.forensics: Vidjil sequence analysis implemented.
• Browser.questions: abundance filtering after sample subtraction now based on complete data, instead of only subtracted sample.
• Browser.questions: fixes and improvements for sample subtraction (available in advanced user mode).
• Browser.questions: minor vis improvements (e.g. tooltips) for sample subtraction.
• Pipeline: incomplete junctions: junction classes DD:Db-Db, DD:Dd3-Dd2, DJ:Dd3-Jd, VD:Vb-Db, VD:Va-Dd3, VD:Vd-Dd2 are now considered known (from capture data, to be monitored), i.e. we have removed their 'unk' tag (i.e. we were still reporting them previously, but e.g. like this: "unkDD:Db-Db").
• Pipeline: incomplete junctions: improvement in D annotation (in DD and DJ junction classes).
• Pipeline: improvements in the capture module.

0.19.501 | 05.02.17

• Pipeline: 'rearrangement' of code to handle big data - TBC.
• Pipeline: IMGT/V-QUEST reference directory release: 201649-4 (8 December 2016).
• Browser: improved messages.
• This changelog: now showing the date the log was written.

0.19.001 | 30.01.17

• Browser.processing: tooltip for paired-end reads FASTQ files uploading.
• Browser: minor over-all improvements.
• Pipeline: safer paired-end reads processing.

0.19.000 | 01.12.16

• Browser: 'user mode' widget moved to the left (i.e. is part of the page header now).
• Browser: compatibility with new version of 'data.table' (1.9.8) R-package.
• Browser.processing: new text-input widget for text to use tracer sequences just by copy-pasting them (in FASTA format).
• Browser.forensics.lineup: UI font/style improvements.
• Browser.forensics.network: UI simplifications.
• Pipeline: incomplete junctions: better sensitivity.
• Pipeline: incomplete junctions: fixed bug affecting IGHD1-26*01, IGHD2-2*02, IGHD2-21*02.
• Pipeline: better coordinates for TR[ABD]J germlines with missing 2nd anchor / GXG motif.

0.18.002 | 16.11.16

• Browser.forensics: automatic threshold finding improvement.
• Browser: minor bug fixes and improvements across all panels.

0.18.001 | 31.10.16

• Browser.questions: combinations 5' and 3' genes and primers now available as single feature types.
• Browser: minor bug fixes and improvements.

0.18.000 | 27.10.16

• Browser.forensics.network: improved sequence alignment in static infobox.
• Browser.forensics.network: improved hover infobox.
• Browser.forensics: minor bug fixes and improvements.
• Browser.questions: 'functionality' now available as a filter and feature type, 'functionality comment' as a feature type.
• Browser.questions: virtual in-frame gaps can now be removed from 'junction nt sequence', also affecting 'junction nt length'.
• Pipeline: safer choice of 3' gene.
• Pipeline: IGKJ2's 2nd anchor was offset by 1nt, causing virtual in-frame gaps in some cases.
• Pipeline: IMGT compatibility: identical distal sequences are now used like any other.
• Pipeline: IMGT compatibility: gene and allele name ordering to match IMGT's.
• Pipeline: IMGT compatibility: now taking P nt into account for virtual in-frame gaps.

0.17.000 | 08.10.16

• *: 'target' to 'tracer' (for rearrangement of interest) across the platform.
• Browser.forensics.lineup: better (incl. showing more informative alignments), faster.
• Browser.forensics: UI clean-up for simple user mode.
• Browser: minor bug fixes and improvements across all panels.
• Pipeline: implemented 'no primer, no junction' logic - tbd.
• Pipeline: now ignoring D alignment with both 5' and 3' heptamers.
• Pipeline: minor bug fixes (better handling of extreme cases).
• Pipeline: further improvements of the capture module.

0.16.002 | 02.10.16

• Browser.forensics.network: major interface re-design, and quick-guide update - more to come soon.
• Pipeline: improved ALARM hints and tips.

0.16.001 | 29.09.16

• Browser: small fix on 'details' table rendering.
• Browser: new 'remove # from nt junctions' checkbox in 'questions' panel in 'advanced' user mode.
• Browser.forensics.network: clone color legend included in the table even for 'other tracers'.
• Pipeline: better handling of failed samples with no .clntab files.

0.16.000 | 26.09.16

• Browser: small fix on 'table' tooltips.
• Browser: cleaner nomenclature around targets (now 'tracers').
• Browser.forensics.network: lineup row select fix.
• Browser.forensics.network: pop-up window with tips & notes.
• Browser.forensics.network: fixed differences in alignment between lineup and 'clicked info box'.
• Pipeline: minor improvements all around, incl. in logging/reporting and workflow.
• Pipeline: further major improvements of the capture module, esp. on reducing false positives - tbc.

0.15.001 | 20.09.16

• Pipeline: more flexible handling of gzipped FASTQs.
• Browser: small fix on 'table' tooltips.

0.15.000 | 19.09.16

• Pipeline: handling NextSeq per-lane FASTQs.
• Pipeline: improved capture module, incl. bloom pre-filtering for speed.

0.14.001 | 16.09.16

• Browser.forensics.network: major improvements in usability, more info on selected nodes, comparison mode.
• Browser.questions: reminder note to switch to 'advanced' user mode for more widgets.
• Browser: multiple bug and crash fixes.
• Pipeline: HTML email with smaller fixed-width font.
• Pipeline: check for FASTQs with wrong number of lines.

0.14.000 | 07.09.16

• From now on we'll try and keep this changelog accurately up-to-date.
• Major changes in the browser included the re-implementation of "user modes", multiple updates of the 'forensics' panel, improvements and bug fixes in 'questions', and introduction of new and improvement of old functionalities in 'file' and 'processing'.
• Over the past few updates, major pipeline (WMD) changes included work on primer annotation in special cases, controlling oversensitivity of junction finding, and tracing targets - the effect on results for our test sets was essentially zero.
• Started this changelog. Versions: 1st numeric part = milestone releases; 2nd = major changes, mostly affecting results; 3rd = minor changes.