 eugenefischer
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16daf02dd6
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Merge branch 'Dev_Vertex'
# Conflicts:
# src/main/java/GraphModificationFunctions.java
# src/main/java/GraphWithMapData.java
# src/main/java/Simulator.java
# src/main/java/Vertex.java
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2022-09-25 18:33:26 -05:00 |
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eugenefischer
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740835f814
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fix typo
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2022-09-25 17:47:07 -05:00 |
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eugenefischer
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8a77d53f1f
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Output sequence counts before and after pre-filtering (currently pre-filtering only sequences present in all wells)
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2022-09-25 17:20:50 -05:00 |
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eugenefischer
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58fa140ee5
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add comments
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2022-09-25 16:10:17 -05:00 |
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eugenefischer
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475bbf3107
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Sort vertex lists by vertex label before making adjacency matrix
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2022-09-25 15:54:28 -05:00 |
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eugenefischer
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4f2fa4cbbe
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Pre-filter saturating sequences only. Retaining singletons seems to improve matching accuracy in high sample rate test (well populations 10% of total cell sample size)
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2022-09-25 15:19:56 -05:00 |
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eugenefischer
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58d418e44b
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Pre-filter saturating sequences only. Retaining singletons seems to improve matching accuracy in high sample rate test (well populations 10% of total cell sample size)
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2022-09-25 15:06:46 -05:00 |
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eugenefischer
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1971a96467
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Remove pre-filtering of singleton and saturating sequences
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2022-09-25 14:55:43 -05:00 |
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eugenefischer
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e699795521
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Revert "by-hand merge of needed code from custom vertex branch"
This reverts commit 29b844afd2.
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2022-09-25 14:34:31 -05:00 |
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eugenefischer
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61d1eb3eb1
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Revert "Reword output message"
This reverts commit 63317f2aa0.
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2022-09-25 14:34:31 -05:00 |
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eugenefischer
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cb41b45204
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Revert "Reword option menu item"
This reverts commit 06e72314b0.
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2022-09-25 14:34:31 -05:00 |
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eugenefischer
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a84d2e1bfe
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Revert "Add comment on map data encodng"
This reverts commit 73c83bf35d.
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2022-09-25 14:34:31 -05:00 |
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eugenefischer
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7b61d2c0d7
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Revert "update version number"
This reverts commit e4e5a1f979.
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2022-09-25 14:34:31 -05:00 |
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eugenefischer
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56454417c0
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Revert "Restore pre-filtering of singleton and saturating sequences"
This reverts commit 5c03909a11.
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2022-09-25 14:34:31 -05:00 |
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eugenefischer
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8ee1c5903e
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Merge branch 'master' into Dev_Vertex
# Conflicts:
# src/main/java/GraphMLFileReader.java
# src/main/java/InteractiveInterface.java
# src/main/java/Simulator.java
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2022-09-25 14:18:56 -05:00 |
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eugenefischer
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5c03909a11
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Restore pre-filtering of singleton and saturating sequences
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2022-09-22 01:39:13 -05:00 |
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eugenefischer
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e4e5a1f979
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update version number
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2022-09-22 00:00:02 -05:00 |
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eugenefischer
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73c83bf35d
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Add comment on map data encodng
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2022-09-21 21:46:00 -05:00 |
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eugenefischer
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06e72314b0
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Reword option menu item
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2022-09-21 21:43:47 -05:00 |
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eugenefischer
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63317f2aa0
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Reword output message
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2022-09-21 18:08:52 -05:00 |
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eugenefischer
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29b844afd2
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by-hand merge of needed code from custom vertex branch
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2022-09-21 16:48:26 -05:00 |
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eugenefischer
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dea4972927
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remove prefiltering of singletons and saturating sequences
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2022-09-21 16:09:08 -05:00 |
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eugenefischer
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9ae38bf247
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Fix bug in correct match counter
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2022-09-21 15:59:23 -05:00 |
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eugenefischer
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cf771ce574
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parameterized sequence indices
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2022-09-21 13:15:49 -05:00 |
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 efischer
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1df86f01df
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parameterized sequence indices
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2022-03-05 12:03:31 -06:00 |
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efischer
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96ba57d653
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Remove singleton sequences from wells in initial filtering
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2022-03-04 16:14:17 -06:00 |
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efischer
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b602fb02f1
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Remove obsolete comments
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2022-03-02 23:35:24 -06:00 |
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efischer
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4c872ed48e
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Add optional stdout print flags
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2022-03-01 15:27:04 -06:00 |
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efischer
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3fc39302c7
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Add detail to error message
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2022-03-01 15:24:14 -06:00 |
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efischer
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578bdc0fbf
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clarify help menu text
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2022-03-01 15:08:43 -06:00 |
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efischer
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8275cf7740
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Check for finite pairing error rate
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2022-03-01 09:01:53 -06:00 |
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efischer
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64209691f0
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Check for finite pairing error rate
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2022-03-01 09:00:58 -06:00 |
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efischer
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9fb3095f0f
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Clarify help text
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2022-03-01 08:40:34 -06:00 |
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efischer
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25acf920c2
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Add version information
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2022-03-01 08:34:35 -06:00 |
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efischer
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e04d2d6777
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Fix typos in help menu
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2022-03-01 08:16:06 -06:00 |
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efischer
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3e41afaa64
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bugfix
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2022-02-27 19:08:29 -06:00 |
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efischer
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bc5d67680d
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Add flag to print metadata to stdout
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2022-02-27 17:36:23 -06:00 |
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efischer
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f2347e8fc2
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check verbose flag
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2022-02-27 17:35:50 -06:00 |
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efischer
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c8364d8a6e
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check verbose flag
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2022-02-27 17:34:20 -06:00 |
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efischer
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b1155f8100
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Format -help CLI option
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2022-02-27 16:53:46 -06:00 |
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efischer
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12b003a69f
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Add -help CLI option
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2022-02-27 16:45:30 -06:00 |
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efischer
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32c5bcaaff
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Deactivate file I/O announcement for CLI
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2022-02-27 16:16:24 -06:00 |
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efischer
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2485ac4cf6
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Add getters to MatchingResult
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2022-02-27 16:15:26 -06:00 |
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efischer
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05556bce0c
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Add units to metadata
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2022-02-27 16:08:59 -06:00 |
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efischer
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a822f69ea4
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Control verbose output
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2022-02-27 16:07:17 -06:00 |
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efischer
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3d1f8668ee
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Control verbose output
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2022-02-27 16:03:57 -06:00 |
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efischer
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40c743308b
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Initialize wells
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2022-02-27 15:54:47 -06:00 |
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efischer
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5246cc4a0c
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Re-implement command line options
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2022-02-27 15:35:07 -06:00 |
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efischer
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a5f7c0641d
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Refactor for better encapsulation with CellSamples
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2022-02-27 14:51:53 -06:00 |
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efischer
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8ebfc1469f
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Refactor plate to fill its own wells in its constructor
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2022-02-27 14:25:53 -06:00 |
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