eugenefischer
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cda25a2c62
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Update performance section and TODO
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2022-10-01 18:12:33 -05:00 |
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eugenefischer
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bde6da3076
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fix typo
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2022-10-01 16:12:21 -05:00 |
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eugenefischer
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2eede214c0
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fix typo
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2022-10-01 16:11:32 -05:00 |
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eugenefischer
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98ce708825
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Remove questionable claim, reorder simulation experiments
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2022-10-01 15:46:22 -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Remove outdated comments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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89295777ef
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Update output example
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2022-10-01 14:30:46 -05:00 |
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eugenefischer
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99c92e6eb5
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Update TODO
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2022-10-01 14:21:23 -05:00 |
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eugenefischer
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b82176517c
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Update TOC, command line options
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2022-10-01 13:59:03 -05:00 |
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eugenefischer
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0657db5653
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tyoo
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2022-10-01 13:44:17 -05:00 |
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eugenefischer
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9f0ac227e2
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Clarify steps and reasoning behind the algorithm
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2022-10-01 13:43:14 -05:00 |
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eugenefischer
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54896bc47f
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Correct typo, remove redundant information
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2022-10-01 13:01:44 -05:00 |
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eugenefischer
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b19a4d37c2
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Update readme with newer results, new menu options
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2022-10-01 13:00:33 -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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19badac92b
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Correct misstatement of filter condition in Algorithm section
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2022-09-29 18:32:42 -05:00 |
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eugenefischer
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633334a1b8
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Update Theory section, add Contents and Algorithm section.
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2022-09-29 18:30:07 -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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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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756e5572b9
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update readme
v4.1
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2022-09-29 00:00:19 -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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a19525f5bb
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update readme
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2022-09-28 23:01:59 -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
v4.0
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2022-09-28 03:01:52 -05:00 |
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eugenefischer
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3a47efd361
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Update TODO
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2022-09-28 03:01:03 -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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