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Update to TASBE 5 - #1

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jakebeal wants to merge 934 commits into

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TASBE:master

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Update to TASBE 5#1
jakebeal wants to merge 934 commits into
LivingComputingProject:masterfrom
TASBE:master

This pull request is big! We're only showing the most recent 250 commits

Commits on Jan 21, 2019
- make au_to_ERF correctly distinguish FSC and SSC channels
  jakebeal
  committed
  1b3cd15
- Merge pull request #381 from TASBE/features/removalcounts
  jakebeal
  authored
  d30e112
Commits on Jan 22, 2019
- add validation that nothing is dropped when setPemDropThreshold is zero
  jakebeal
  committed
  f958d4b
- Merge pull request #382 from TASBE/features/pemdroptest
  jakebeal
  authored
  da4e880
Commits on Jan 24, 2019
- add sanitization to peak ID channel
  jakebeal
  committed
  6c037bd
- don't create a legend in octave if there aren't any data points: it bombs
  jakebeal
  committed
  3cf4180
Commits on Jan 27, 2019
- Merge pull request #385 from TASBE/fix/sanitiztionpatch
  jakebeal
  authored
  32077b4
- warn if FCS file is unusually small
  jakebeal
  committed
  0f6de9a
- Merge pull request #386 from TASBE/fix/issue.383
  jakebeal
  authored
  02b576f
- record amount of data gated away and amount not included in histogram, as well as number used in histogram and original raw number
  jakebeal
  committed
  4ef525c
- Merge pull request #387 from TASBE/fix/issue.236
  jakebeal
  authored
  a4b1866
- multi-dimensional autogating appears to now be working correctly
  jakebeal
  committed
  6bfd02d
- Merge pull request #388 from TASBE/fix/issue.96
  jakebeal
  authored
  8add742
Commits on Jan 28, 2019
- Correct bug that caused TASBE to ignore peak ID forcing on size beads
  jakebeal
  committed
  382eb23
- Merge pull request #390 from TASBE/fix/issue.389
  jakebeal
  authored
  412b62e
- improve size/filtering error messages and controllability
  jakebeal
  committed
  59fa86f
- fix broken aggregator in event checking
  jakebeal
  committed
  d033116
Commits on Jan 29, 2019
Commits on Feb 4, 2019
- use the warning switching facility to switch notify/succeed/skip
  jakebeal
  committed
  33f1dc0
- Merge pull request #394 from TASBE/fix/issue.393
  jakebeal
  authored
  7a36765
- fix typo
  jakebeal
  committed
  7aba85f
Commits on Feb 5, 2019
- Merge pull request #395 from TASBE/develop
  jakebeal
  authored
  764249e
- update version for release
  jakebeal
  authored
  e82e9c7
- update pre-release version in develop
  jakebeal
  committed
  0354f0e
- Add warning when units other than MEFL are selected for bead calibration
  jakebeal
  committed
  724fc06
Commits on Feb 6, 2019
- Merge pull request #396 from TASBE/fix/issue.143
  jakebeal
  authored
  29ed2c4
Commits on Feb 14, 2019
- more informative warnings in fca_readfcs
  jakebeal
  committed
  b59cdff
- Fix issue #400
  jakebeal
  committed
  4d83489
- Merge pull request #401 from TASBE/fix/issue.400
  jakebeal
  authored
  c4247bd
- turn off channel disambiguation warning
  jakebeal
  committed
  2107516
- Merge pull request #403 from TASBE/fix/issue.384
  jakebeal
  authored
  2413307
Commits on Feb 26, 2019
- Addressed issues #398 and #397
  coverney
  committed
  dc1a899
- Changed JSON encoding and decoding to work with Octave
  coverney
  committed
  981d3fd
- Fixed empty string problem
  coverney
  committed
  ff199c5
- Made fca_readcsv compatible with octave
  coverney
  committed
  3bc9db0
Commits on Feb 27, 2019
- set stem name before running ```per_color_constitutive_analysis```
  coverney
  committed
  28fd316
- Merge branch 'develop' into coverney.issue397
  Cassandra Overney
  authored
  c47b5c3
- Copied original test_fca_reading file
  coverney
  committed
  38ca6e0
- typo fix
  jakebeal
  committed
  5c50178
- restored use of flow.maxEvents
  jakebeal
  committed
  959acda
- Merge pull request #408 from TASBE/coverney.issue397
  jakebeal
  authored
  04fb3a0
Commits on Feb 28, 2019
- Added CSVReaderHeader config and tested it with the tutorial
  coverney
  committed
  132481a
- Merge pull request #412 from TASBE/coverney.issue410
  jakebeal
  authored
  9e5f5b2
- Merge branch 'develop' of https://github.com/TASBE/TASBEFlowAnalytics into develop
  jakebeal
  committed
  8125c8b
Commits on Mar 3, 2019
- warn when too few size beads
  jakebeal
  committed
  e99798f
- add URQP-38-6K, fixing #406
  jakebeal
  committed
  3b46c06
- Merge pull request #413 from TASBE/fix/issue.405
  jakebeal
  authored
  0a117e0
- Merge pull request #414 from TASBE/develop
  jakebeal
  authored
  ead8f7e
- Update version.txt
  jakebeal
  authored
  2a5fa14
Commits on Mar 5, 2019
- Added structs to JSON header
  coverney
  committed
  49543a8
- Added JSON header from tutorial to test directory
  coverney
  committed
  4e5c2e6
- Fixed little typo in ```test_csv_reading```
  coverney
  committed
  7c0f3fe
- Addressed issue #407
  coverney
  committed
  f65159f
Commits on Mar 12, 2019
- Wrote test for batch_analysis_csv
  coverney
  committed
  0c7eb41
- Updated expected point cloud to match with tutorial
  coverney
  committed
  5c690d7
- Merge pull request #416 from TASBE/coverney.issue415
  jakebeal
  authored
  3ab08c4
- Merge pull request #419 from TASBE/develop
  jakebeal
  authored
  2c9f508
- Update version.txt
  jakebeal
  authored
  8ccb500
- update development version
  jakebeal
  committed
  048c2bb
- Merge branch 'develop' into coverney.issue407
  coverney
  committed
  651e85a
Commits on Mar 13, 2019
- Fixed batch analysis octave bug
  coverney
  committed
  39c83c0
- Fixed test_batch_output_excel octave bug
  coverney
  committed
  9c3fc70
- Merge pull request #418 from TASBE/coverney.issue407
  jakebeal
  authored
  dab8a6e
Commits on Mar 20, 2019
- Created DataFile objects and updated tests
  coverney
  committed
  fb7f58a
Commits on Mar 25, 2019
- Fix issue #422, test to ensure fix is in
  jakebeal
  committed
  eff8427
- Merge pull request #423 from TASBE/fix/issue.422
  jakebeal
  authored
  d1399f2
Commits on Mar 26, 2019
- Fixed getExcelFilename bug when making colormodel from excel
  coverney
  committed
  7074de2
- Merge branch 'develop' into coverney.issue411
  coverney
  committed
  263baae
- Fixed bug when writing point cloud files
  coverney
  committed
  d25a2a5
- Fixed logical operator comparison bug
  coverney
  committed
  c75e927
Commits on Mar 28, 2019
- reproduce issue 420 in a test; also fix an issue for older Matlab reading tables
  jakebeal
  committed
  7ef6823
- added fcs_channel constructor, using it to ensure fields all get populated during CSV reads
  jakebeal
  committed
  c9809a5
- csv reading now testing successfully
  jakebeal
  committed
  bf2ada4
- add in fcs 3.1 field that was causing trouble
  jakebeal
  committed
  6abb0b8
- Merge pull request #427 from TASBE/fix/issue.420
  jakebeal
  authored
  2c33083
Commits on Apr 2, 2019
- Addressed requested changes
  coverney
  committed
  2e79b50
- Merge pull request #424 from TASBE/coverney.issue411
  jakebeal
  authored
  5926f9d
- Addressed issue #425
  coverney
  committed
  00c0523
- Merge branch 'develop' into coverney.issue411
  coverney
  committed
  43989ea
- Fixed csv reading test
  coverney
  committed
  ab544c9
Commits on Apr 3, 2019
- Merge pull request #430 from TASBE/coverney.issue425
  jakebeal
  authored
  1a07db8
- Changed to canonical pathnames in CSV header filename matching
  coverney
  committed
  90b1a18
- Merge pull request #431 from TASBE/coverney.issue426
  jakebeal
  authored
  ef9fc67
- Ensure that flow.channel_template_file gets wrapped into a DataFile object when used by resolve
  jakebeal
  committed
  3cb34e2
- Merge pull request #433 from TASBE/fix/datafile-in-resolve
  jakebeal
  authored
  b98965a
Commits on Apr 4, 2019
- add zero-argument constructor
  jakebeal
  committed
  6233a0c
- Merge pull request #434 from TASBE/fix/issue.432
  jakebeal
  authored
  5caefc2
- ensure batch analysis DataFile conversions
  jakebeal
  committed
  c1855e6
- fail faster and with a clearer error message when beads are missing
  jakebeal
  committed
  c470b62
- Merge pull request #435 from TASBE/fix/issue.432
  jakebeal
  authored
  cca002d
- Merge pull request #436 from TASBE/fix/failfast-on-missing-beadfile
  jakebeal
  authored
  b5d1e70
Commits on Apr 9, 2019
- make autofluorescence models use TASBEconfig, refactor
  jakebeal
  committed
  f1c1d99
- update autofluorescence model documentation
  jakebeal
  committed
  85bb8bf
Commits on Apr 10, 2019
- Addressed #421 and #409
  coverney
  committed
  f2b9915
Commits on Apr 11, 2019
- Merge pull request #437 from TASBE/coverney.issue421
  jakebeal
  authored
  ebf6348
Commits on Apr 13, 2019
- improve clarity
  jakebeal
  committed
  00154be
- Update README to fix #124
  jakebeal
  committed
  6c562ce
Commits on Apr 14, 2019
- Reviewed all label commands, so all that need units have units. Fix #9.
  jakebeal
  committed
  b0fdb13
- use TASBEConfig for cm_scatter and fcs_scatter figure sizes
  jakebeal
  committed
  9ec9172
- AutogateParameters --> TASBEConfig
  jakebeal
  committed
  99f6123
- use output figure size in plots
  jakebeal
  committed
  37b6a55
- compensations use figure size
  jakebeal
  committed
  ba77fa2
- Merge pull request #439 from TASBE/fix/issue.9
  jakebeal
  authored
  669b8eb
Commits on Apr 15, 2019
- finished figure resizing, expansion of TASBEConfig
  jakebeal
  committed
  8d1c067
- Merge branch 'develop' into fix/issue.429
  jakebeal
  committed
  ea9cb6d
- fix bad merge
  jakebeal
  committed
  d9eee1c
- remove obsolete commands
  jakebeal
  committed
  aafead3
- working on handling of derived channels
  jakebeal
  committed
  e7e4110
- updated obsolete AutofluorescenceModel constructor
  jakebeal
  committed
  5f50a1c
- allow derived channels for color models
  jakebeal
  committed
  87655eb
- Merge pull request #440 from TASBE/fix/issue.429
  jakebeal
  authored
  e5b2b72
- Merge branch 'develop' into fix/issue.428
  jakebeal
  committed
  95b802d
- generalized to enable reading of synthetic channels
  jakebeal
  committed
  749540a
- fix bad pointer in test
  jakebeal
  committed
  7bb90f5
- deal with octave vs. matlab difference in handling mean([])
  jakebeal
  committed
  d9ddfdc
- fix stupid typo
  jakebeal
  committed
  3dc0d6c
- octave std doesn't do weighting, made a weighted version
  jakebeal
  committed
  3e1ac21
- Merge pull request #441 from TASBE/fix/issue.428
  jakebeal
  authored
  f3e1102
Commits on Apr 16, 2019
- Updated TASBEConfig sheet
  coverney
  committed
  c6bf59a
- Merge pull request #445 from TASBE/coverney.issue444
  jakebeal
  authored
  7b5a7a2
Commits on Apr 17, 2019
- Added test_colormodel_csv
  coverney
  committed
  dce03b3
- Fixed error with pathnames
  coverney
  committed
  d9f1338
- Updated colormodel csv filenames
  coverney
  committed
  f52bce5
- removed test_colormodel_warnings
  coverney
  committed
  cf63f4e
Commits on Apr 22, 2019
- make sure postfilters can be applied to already-unit-converted CSV files
  jakebeal
  committed
  2cd8d0b
- Merge pull request #447 from TASBE/fix/postfilter_csv
  jakebeal
  authored
  f6a5814
Commits on Apr 24, 2019
- fix sample stat sizes to prevent shaping issue with all-blank samples
  jakebeal
  committed
  099a7c4
- Merge pull request #448 from TASBE/fix/allblank-shaping
  jakebeal
  authored
  8e4df09
- Added channelMaximum to TASBEConfig
  coverney
  committed
  9f5cccf
- Fixed typo in computeColorTranslations
  coverney
  committed
  95a43cc
- add returns to config checkpointing to decrease test cross-contamination
  jakebeal
  committed
  c062ec9
- Merge pull request #446 from TASBE/coverney.issue399
  jakebeal
  authored
  2e339cf
- shorten the amount of samples handled in some tests
  jakebeal
  committed
  327e890
- warn on setting a previously unknown configuration key
  jakebeal
  committed
  a5ab9ee
- Merge pull request #451 from TASBE/develop
  jakebeal
  authored
  e8fdc94
- Merge pull request #450 from TASBE/shorten-tests
  jakebeal
  authored
  a4e8ab3
- Update version.txt
  jakebeal
  authored
  7cbb218
- Merge branch 'master' into develop
  jakebeal
  committed
  061587f
- update development version
  jakebeal
  committed
  987e91a
- Merge pull request #452 from TASBE/fix/issue.443
  jakebeal
  authored
  9e483ce
- Attempt to fix range issue by reading whole first sheet rather than a specific range in it.
  jakebeal
  committed
  ea80675
- Merge pull request #453 from TASBE/fix/issue.171
  jakebeal
  authored
  ee221c5
Commits on Apr 26, 2019
- Added channelMaximum to test_colormodel
  coverney
  committed
  6d35d30
- Merge pull request #449 from TASBE/coverney.issue252
  jakebeal
  authored
  d005ab7
Commits on Apr 28, 2019
- Allow gate components to be selected by location as well as by ID, which will fix #159
  jakebeal
  committed
  1c3a8d8
- refactor csv reading to separate header and data reads
  jakebeal
  committed
  282d307
Commits on Apr 29, 2019
- more userful refactoring; 438 may not move forward farther, however.
  jakebeal
  committed
  e26feba
- Merge pull request #454 from TASBE/fix/issue.159
  jakebeal
  authored
  32b4011
- Merge pull request #455 from TASBE/fix/issue.438
  jakebeal
  authored
  33e7faf
Commits on Apr 30, 2019
- Addressed issue #359
  coverney
  committed
  9b2c550
- Made suggested changes
  coverney
  committed
  5d50aad
- Fixed gating test
  coverney
  committed
  1371306
- Merge pull request #456 from TASBE/coverney.issue359
  jakebeal
  authored
  14f914c
Commits on May 6, 2019
- Addressed issue #360
  coverney
  committed
  d09fa37
- Merge branch 'develop' into coverney.issue360
  Cassandra Overney
  authored
  398c729
- Merge pull request #457 from TASBE/coverney.issue360
  jakebeal
  authored
  0b15380
- avoid false "high gating variation" warnings triggered by not using a gate
  jakebeal
  committed
  0241cc0
Commits on May 7, 2019
- Merge pull request #458 from TASBE/fix/avoid-zero-gating-warnings
  jakebeal
  authored
  41ebefb
- Modified code structure to be more efficient
  coverney
  committed
  a64cf3a
- Merge pull request #459 from TASBE/coverney.issue360
  jakebeal
  authored
  e32f921
- Merge pull request #461 from TASBE/develop
  jakebeal
  authored
  af4d3b0
- Update version.txt
  jakebeal
  authored
  66101ea
Commits on May 13, 2019
- Added print name checking to read csv
  coverney
  committed
  ff9a2a1
- Added tests for issue #460
  coverney
  committed
  5136fa5
- List channel options when channel name not found
  coverney
  committed
  6e19c95
Commits on May 14, 2019
- Added print names to colormodel_csv.json
  coverney
  committed
  fd428d7
- Merge pull request #463 from TASBE/coverney.issue347
  jakebeal
  authored
  c7edfbe
- Merge pull request #462 from TASBE/coverney.issue460
  jakebeal
  authored
  bd42cf4
Commits on Jun 5, 2019
- fixed a matlab reading bug, partial fix of #467
  jakebeal
  committed
  fe0204a
- modification of colormodel_csv.json to exercise issues #466 and #467
  jakebeal
  committed
  97bd993
Commits on Jun 8, 2019
- Addressed issues #467 and #466
  coverney
  committed
  d47f1a8
- Added a more foolproof solution to issues #467 and #466
  coverney
  committed
  7fd519d
Commits on Jun 9, 2019
- Merge pull request #468 from TASBE/coverney.issue467
  jakebeal
  authored
  a8630f9
Commits on Jun 11, 2019
- update citation in author and readme file
  jakebeal
  committed
  745d3b4
Commits on Jun 14, 2019
- Merge branch 'master' of https://github.com/TASBE/TASBEFlowAnalytics
  jakebeal
  committed
  9c810a8
Commits on Jun 22, 2019
- Addressed issue #356
  coverney
  committed
  f91f7e3
- Addressed issue #469
  coverney
  committed
  8710179
- Added test for batchResults
  coverney
  committed
  c6ac81e
- Fixed reference to `InducerLevelsToFiles`
  coverney
  committed
  1787d51
- Merge pull request #474 from TASBE/coverney.issue469
  jakebeal
  authored
  89773a3
- Changed output of `writeBatchResults` to actual data instead of csv file
  coverney
  committed
  6d5158f
- Merge pull request #473 from TASBE/coverney.issue356
  jakebeal
  authored
  4e9c9e2
Commits on Jun 23, 2019
- Update version.txt
  jakebeal
  authored
  c4d20e4
- Merge branch 'master' into develop
  jakebeal
  authored
  f180e8f
- Merge pull request #475 from TASBE/develop
  jakebeal
  authored
  2495d01
Commits on Jun 24, 2019
- update to next alpha version
  jakebeal
  committed
  40eb037
Commits on Jun 29, 2019
- Addressed issue #470
  coverney
  committed
  567f010
- Fixed test because added Config to bottom of plots
  coverney
  committed
  997b0b2
- Merge pull request #477 from TASBE/coverney.issue470
  jakebeal
  authored
  4418c26
Commits on Sep 4, 2019
- add ACS SynBio TASBE publication reference
  jakebeal
  authored
  01a0d57
Commits on Sep 5, 2019
- check if xenial vs. trusty is causing the crash
  jakebeal
  committed
  dad6a47
- attempt migration to xenial on travis
  jakebeal
  committed
  9d43e16
- Merge pull request #479 from TASBE/bug/xenial-v-trusty
  jakebeal
  authored
  d313e0e
- import travis xenial patch used in develop
  jakebeal
  authored
  1bd6a6e
Commits on Sep 27, 2019
- correct "SPILL" to "SPILLOVER" in fca_readfcs.m
  jakebeal
  committed
  16c6906
- make fcs_channel_names tolerant to both string and DataFile call
  jakebeal
  committed
  b755e37
- Merge pull request #483 from TASBE/fix/fca-spillover
  jakebeal
  authored
  39f1630
- Merge pull request #484 from TASBE/develop
  jakebeal
  authored
  198c266
- Update version for release
  jakebeal
  authored
  89b3204
Commits on Oct 2, 2019
- Updated README
  Cassandra Overney
  authored
  ce85d99
- Update README
  Cassandra Overney
  authored
  e482c6b
- Merge pull request #485 from TASBE/coverney.issue481
  jakebeal
  authored
  60422f5
- Addressed issues #480 and #482
  coverney
  committed
  755bc0e
Commits on Oct 3, 2019
- Merge pull request #486 from TASBE/coverney.issue482+480
  jakebeal
  authored
  1c0ae4d
Commits on Dec 14, 2019
- Edited TASBEConfig and TASBESession for #292
  Cassandra Overney
  committed
  df68560
Commits on Dec 15, 2019
- Wrote TASBESession error_silent function for excel interface
  coverney
  committed
  29fc3a7
Commits on Dec 16, 2019
- Fixed bug in `test_errors_excel`
  coverney
  committed
  1fcf022
- Continue to fix bug in test_excel_errors
  coverney
  committed
  fca39e8
- Continue to fix bug in `test_errors_excel`
  coverney
  committed
  adec87b
- Continue to fix bug in `test_errors_excel`
  coverney
  committed
  4fabddc
- Continuing to fix bug in test_errors_excel
  coverney
  committed
  921098d
- Merge pull request #488 from TASBE/coverney.issue292
  jakebeal
  authored
  5cb5039
Commits on Jan 14, 2020
- Merge pull request #493 from TASBE/develop
  jakebeal
  authored
  bd9f224
- release 8.3.0
  jakebeal
  authored
  b80b6ad
- Release 8.3.0
  jakebeal
  authored
  e477b36
- Prepare develop for alpha of next version
  jakebeal
  committed
  3d0aef2
Commits on Mar 12, 2020
- added SpheroTech URCP-38-2K lot AL02
  jakebeal
  committed
  a4c55fe
Commits on May 8, 2020
- fix issue #494, also use previously ignored minimumBinCount variable
  jakebeal
  committed
  1c38547
- Merge pull request #499 from TASBE/fix/issue.494
  jakebeal
  authored
  ed0274d
- Merge pull request #500 from TASBE/develop
  jakebeal
  authored
  732aaea
- Update version.txt
  jakebeal
  authored
  8d012fe
Commits on Jul 22, 2020
- add link to iGEM
  jakebeal
  authored
  7c9d0a3
Commits on Sep 11, 2020
- fix FCS read handling of very small files
  jakebeal
  committed
  626e0d7
Commits on Sep 12, 2020
- handle octave crash on empty flow file
  jakebeal
  committed
  b8f64e7
- Merge pull request #506 from TASBE/fix/issue-505
  jakebeal
  authored
  d120c8e
Commits on Sep 17, 2020
- add a second test
  Jake Beal
  committed
  d66b6e4
Commits on Sep 18, 2020
- fix test 2
  Jake Beal
  committed
  1e56f58
- additional challenging test
  Jake Beal
  committed
  3cf680b
Commits on Sep 22, 2020
- reproduce and fix SD2 bug
  Jake Beal
  committed
  5f6924b
- Merge pull request #508 from TASBE/fix/issue-505
  jakebeal
  authored
  50a7371
- fix for n-sample case as well
  Jake Beal
  committed
  0d7cc09
- Merge pull request #509 from TASBE/fix/issue-505
  jakebeal
  authored
  8b704e4
- more fundamental fix for the problem in issue #505
  Jake Beal
  committed
  038296b
- Merge pull request #510 from TASBE/505-revisited
  jakebeal
  authored
  14d5727
Commits on Sep 23, 2020
- Merge pull request #507 from TASBE/develop
  jakebeal
  authored
  9a401ad
- Update version.txt
  jakebeal
  authored
  583a291
- push version for development
  Jake Beal
  committed
  f679ef6
Commits on Oct 16, 2020
- fix URQP catalog number and add lot AL01
  Jake Beal
  committed
  3712638
- Merge pull request #513 from TASBE/fix/issue-511
  jakebeal
  authored
  36d27c4
Commits on Nov 24, 2020
- Add additional spherotech 38-2K lots
  Jake Beal
  committed
  4d8b9e2
- Merge pull request #516 from TASBE/develop
  jakebeal
  authored
  7158d21
- Update version.txt
  jakebeal
  authored
  1a56c32
Commits on Feb 17, 2021
- fix a handling of multi-component degenerate Gaussian fits and of empty percentiles
  Jake Beal
  committed
  a50edd9
- Merge pull request #520 from TASBE/fix/multi-component-degenerate-gaussian
  jakebeal
  authored
  0ba070d
Commits on Mar 3, 2021
- Add capability to plot GMMs in batch analyses
  jakebeal
  committed
  d76a933
- Merge pull request #521 from TASBE/batch-plot-GMMs
  jakebeal
  authored
  57a4d85
Commits on Mar 4, 2021
- Merge pull request #522 from TASBE/develop
  jakebeal
  authored
  b72dfae
- Update version.txt
  jakebeal
  authored
  db34233

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