 eugenefischer
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b3273855a6
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Test simpler source/target differentiation
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2022-10-14 18:11:21 -05:00 |
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eugenefischer
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51c1bc2551
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Skip edges with zero weight
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2022-10-14 18:09:34 -05:00 |
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eugenefischer
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f7d522e95d
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Comment out old MWM algorithm, add auction algorithm
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2022-10-14 17:38:07 -05:00 |
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eugenefischer
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5f0c089b0a
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add getter for matchingWeight
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2022-10-14 17:37:40 -05:00 |
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eugenefischer
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d3066095d9
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add getter/setter for potential
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2022-10-14 17:32:37 -05:00 |
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eugenefischer
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55a5d9a892
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Making fields final
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2022-10-14 17:32:21 -05:00 |
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eugenefischer
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49708f2f8a
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Initial auction algorithm implementation
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2022-10-14 17:31:59 -05:00 |
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eugenefischer
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e7e85a4542
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Comment out questionable claim
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2022-10-01 15:44:29 -05:00 |
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eugenefischer
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c0dd2d31f2
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Update version number
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2022-10-01 15:21:33 -05:00 |
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eugenefischer
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cf103c5223
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Add flag to enable p-value calculation
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2022-10-01 14:36:22 -05:00 |
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eugenefischer
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26f66fe139
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Remove outdated comments
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2022-10-01 14:35:35 -05:00 |
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eugenefischer
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457d643477
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Make calculation of p-values optional, defaulting to off
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2022-09-30 03:17:58 -05:00 |
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eugenefischer
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593dd6c60f
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Add sample cell filename, cell sample size, and sample plate size to metadata
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2022-09-30 02:58:15 -05:00 |
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eugenefischer
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b8aeeb988f
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Add sequence dropout rate to metadata output
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2022-09-30 00:33:41 -05:00 |
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eugenefischer
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b9b13fb75e
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Rename dropout rate flag
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2022-09-29 23:58:08 -05:00 |
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eugenefischer
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289220e0d0
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Remove statements about pre-filtering types. Can add that back if I ever actually parameterize that.
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2022-09-29 22:10:42 -05:00 |
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eugenefischer
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e308e47578
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Correct error in comments
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2022-09-29 18:29:43 -05:00 |
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eugenefischer
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133984276f
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Change access modifiers and add count of wells removed to output
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2022-09-29 16:03:10 -05:00 |
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eugenefischer
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ec6713a1c0
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Implement filtering for wells with anomalous read counts
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2022-09-29 16:03:10 -05:00 |
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 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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