eugenefischer
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7744586e79
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change frequency of garbage collection requests
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2025-04-10 20:07:34 -05:00 |
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eugenefischer
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83eff0d1e7
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remove output to stdout that was added for testing
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2025-04-10 15:08:33 -05:00 |
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eugenefischer
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d1810c453d
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Even more efficient graph creation (my initial scheme, but this time without accidentally changing what's in the sequence records)
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2025-04-10 15:03:10 -05:00 |
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eugenefischer
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187401f2d6
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More efficient graph creation
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2025-04-10 14:06:11 -05:00 |
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eugenefischer
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678ce99424
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iterate over vertex wells correctly
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2025-04-10 13:34:04 -05:00 |
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eugenefischer
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c21e375303
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fix concurrent modification bug
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2025-04-10 13:33:47 -05:00 |
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eugenefischer
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57fe9c1619
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Update graph modification functions to work with edges directly
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2025-04-10 12:42:19 -05:00 |
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eugenefischer
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e1888a99c6
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refactor to construct the bipartite graph directly, rather than by using an adjacency matrix and a graph generator.
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2025-04-10 11:47:15 -05:00 |
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eugenefischer
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b5c0568e22
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Add dependencies
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2025-04-10 10:53:42 -05:00 |
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eugenefischer
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b7597cff2a
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update readme and add Zipf exponent option to CLI
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2025-04-09 16:16:46 -05:00 |
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eugenefischer
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a43ee469ea
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implement Zipf distribution
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2025-04-09 14:32:02 -05:00 |
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eugenefischer
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e686d4957b
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disable selection of the scaling integer weight MWM algorithm via the interactive interface
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2025-04-09 11:20:52 -05:00 |
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eugenefischer
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fbc0496675
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update readme and default heap type
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2025-04-09 11:18:21 -05:00 |
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eugenefischer
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0071cafbbd
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Rough implementation, missing final dual adjustment step, and may have other bugs as well as it does not yet output a maximum weight matching
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2025-04-09 10:17:13 -05:00 |
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eugenefischer
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3d302cf8ad
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initial commit of stub of integer weight scaling algorithm
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2025-03-27 13:42:27 -05:00 |
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eugenefischer
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58cdf9ae93
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Lookback AA implementation, doesn't currently work
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2023-04-09 20:45:03 -05:00 |
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eugenefischer
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96d49d0034
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clarifying comment
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2023-04-09 19:48:43 -05:00 |
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eugenefischer
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70b08e7c22
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Bugfixes and streamlining
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2022-10-22 17:59:01 -05:00 |
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eugenefischer
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44158d264c
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Correct sequence count
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2022-10-22 16:16:32 -05:00 |
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eugenefischer
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e97c2989db
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Add dropout rate calculation to read-in of data from plate file (this may slow down read-in by a lot)
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2022-10-22 16:04:41 -05:00 |
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eugenefischer
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f7709ada73
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Change order of metadata comments
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2022-10-22 15:50:35 -05:00 |
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eugenefischer
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25b37eff48
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renamed to MaximumIntegerWeightBipartiteAuctionMatching
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2022-10-22 15:00:22 -05:00 |
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eugenefischer
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fbbb5a8792
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Update comments
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2022-10-22 14:59:43 -05:00 |
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eugenefischer
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4b9d7f8494
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Add option to select matching algorithm type, rename types in output
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2022-10-22 14:59:24 -05:00 |
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eugenefischer
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0de12a3a12
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Refactor to use selected algorithm type
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2022-10-22 14:58:40 -05:00 |
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eugenefischer
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3c2ec9002e
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Add field for algorithm type, methods to set algorithm type
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2022-10-22 14:13:31 -05:00 |
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eugenefischer
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bcf3af5a83
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Update algorithm type names
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2022-10-22 14:10:00 -05:00 |
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eugenefischer
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fcca22a2f0
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Rename class, modify bidding to include marginal item value
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2022-10-22 13:18:43 -05:00 |
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eugenefischer
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910de0ce9d
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Fix typos
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2022-10-21 13:46:10 -05:00 |
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eugenefischer
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ef349ea5f6
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Correctly store matching weight
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2022-10-14 18:44:56 -05:00 |
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eugenefischer
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174db66c46
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Clean up comments
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2022-10-14 18:31:32 -05:00 |
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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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