 efischer
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097590cf21
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Add method to remove a well from the SequenceRecord (git committed as past self due to IDE misclick)
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2022-09-29 16:03:10 -05:00 |
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 eugenefischer
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f1e4c4f194
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Remove duplicate output statements
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2022-09-29 01:05:36 -05:00 |
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eugenefischer
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b6218c3ed3
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update version
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2022-09-29 00:53:11 -05:00 |
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eugenefischer
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c30167d5ec
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Change real sequence collision so it isn't biased toward sequences in the earlier wells.
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2022-09-28 23:15:55 -05:00 |
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eugenefischer
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e5803defa3
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Bug fix, add comments
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2022-09-28 18:09:47 -05:00 |
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eugenefischer
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34dc2a5721
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Add real sequence collision rate
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2022-09-28 17:54:55 -05:00 |
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eugenefischer
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fd106a0d73
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Add real sequence collision rate
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2022-09-28 17:46:09 -05:00 |
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eugenefischer
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22faad3414
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Add real sequence collision rate
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2022-09-28 17:45:09 -05:00 |
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eugenefischer
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0b36e2b742
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Rewrite countSequences to allow for collision with real sequences on misreads
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2022-09-28 17:44:26 -05:00 |
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eugenefischer
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9dacd8cd34
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Add real sequence collision rate
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2022-09-28 17:43:21 -05:00 |
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eugenefischer
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89687fa849
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Add real sequence collision rate, make fields final
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2022-09-28 17:43:06 -05:00 |
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eugenefischer
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fb443fe958
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Revert "Add getCell and getRandomCell methods"
This reverts commit adebe1542e.
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2022-09-28 14:36:20 -05:00 |
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eugenefischer
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adebe1542e
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Add getCell and getRandomCell methods
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2022-09-28 13:49:50 -05:00 |
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eugenefischer
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882fbfffc6
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Purge old code
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2022-09-28 13:40:13 -05:00 |
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eugenefischer
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a88cfb8b0d
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Add read counts for individual wells to graphml output
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2022-09-28 13:38:38 -05:00 |
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eugenefischer
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deed98e79d
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Bugfix
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2022-09-28 12:58:14 -05:00 |
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eugenefischer
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1a35600f50
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Add method to get read count from individual wells
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2022-09-28 12:57:45 -05:00 |
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eugenefischer
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856063529b
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Read depth simulation is now compatible with plate caching
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2022-09-28 12:47:00 -05:00 |
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eugenefischer
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b7c86f20b3
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Add read depth attributes to graphml output
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2022-09-28 03:01:52 -05:00 |
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eugenefischer
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58bb04c431
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Remove redundant toString() calls
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2022-09-28 02:08:17 -05:00 |
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eugenefischer
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610da68262
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Refactor Vertex class to use SequenceRecords
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2022-09-28 00:58:44 -05:00 |
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eugenefischer
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9973473cc6
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Make serializable and implement getWellOccupancies method
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2022-09-28 00:58:02 -05:00 |
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eugenefischer
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8781afd74c
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Reorder conditional
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2022-09-28 00:57:06 -05:00 |
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eugenefischer
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88b6c79caa
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Refactor to simplify graph creation code
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2022-09-28 00:07:59 -05:00 |
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eugenefischer
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4ad1979c18
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Add read depth simulation options to CLI
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2022-09-27 15:05:50 -05:00 |
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eugenefischer
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423c9d5c93
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Add read depth simulation options to CLI
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2022-09-27 14:35:55 -05:00 |
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eugenefischer
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d71a99555c
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clean up metadata
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2022-09-27 12:15:12 -05:00 |
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eugenefischer
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2bf2a9f5f7
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Add comments
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2022-09-27 11:51:51 -05:00 |
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eugenefischer
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810abdb705
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Add read depth parameters to output metadata
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2022-09-27 11:13:12 -05:00 |
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eugenefischer
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f7b3c133bf
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Add filtering based on occupancy/read count discrepancy
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2022-09-26 23:39:18 -05:00 |
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eugenefischer
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14fcfe1ff3
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spacing
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2022-09-26 23:38:56 -05:00 |
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eugenefischer
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70fec95a00
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Bug fix
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2022-09-26 23:17:18 -05:00 |
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eugenefischer
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077af3b46e
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Clear plate in memory when simulating read depth
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2022-09-26 23:17:10 -05:00 |
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eugenefischer
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db99c74810
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Rework read depth simulation to allow edge weight calculations to work as expected. (This changes sample plate in memory, so caching the sample plate is incompatible)
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2022-09-26 23:03:23 -05:00 |
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eugenefischer
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13a1af1f71
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placeholder values until CLI is updated to support read depth simulation
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2022-09-26 19:43:29 -05:00 |
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eugenefischer
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199c81f983
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Implement read count for vertices
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2022-09-26 19:42:19 -05:00 |
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eugenefischer
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19a2a35f07
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Refactor plate assay methods to use maps passed as parameters rather than returning maps
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2022-09-26 17:00:25 -05:00 |
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eugenefischer
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36c628cde5
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Add code to simulate read depth
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2022-09-26 16:52:56 -05:00 |
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eugenefischer
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1ddac63b0a
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Add exception handling
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2022-09-26 14:28:35 -05:00 |
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eugenefischer
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e795b4cdd0
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Add read depth option to interface
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2022-09-26 14:25:47 -05:00 |
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eugenefischer
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60cf6775c2
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notes toward command line read depth option
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2022-09-26 14:25:30 -05:00 |
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eugenefischer
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8a8c89c9ba
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revert options menu
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2022-09-26 14:24:58 -05:00 |
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eugenefischer
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86371668d5
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Add menu option to activate simulation of read depth and sequence read errors
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2022-09-26 13:47:19 -05:00 |
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eugenefischer
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d81ab25a68
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Comment: need to update this when read count is implemented
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2022-09-26 13:46:53 -05:00 |
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eugenefischer
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02c8e6aacb
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Refactor sequences to be strings instead of integers, to make simulating read errors easier
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2022-09-26 13:37:48 -05:00 |
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eugenefischer
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f84dfb2b4b
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Method stub for simulating read depth
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2022-09-26 00:43:13 -05:00 |
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eugenefischer
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184278b72e
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Add fields for simulating read depth. Also a priority queue for lookback auctions
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2022-09-26 00:42:55 -05:00 |
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eugenefischer
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489369f533
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Add flag to simulate read depth
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2022-09-26 00:42:23 -05:00 |
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eugenefischer
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fbee591273
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Change indentation
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2022-09-25 22:36:02 -05:00 |
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eugenefischer
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d1a56c3578
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Hand-merge of some things from Dev_Vertex branch that didn't make it in for some reason
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2022-09-25 19:07:25 -05:00 |
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