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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603a999b59
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Update readme
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2022-09-25 22:35:52 -05:00 |
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eugenefischer
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c3df4b12ab
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Update readme with read depth TODO
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2022-09-25 21:50:59 -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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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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04a077da2e
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update Readme
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2022-09-25 18:24:12 -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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bd6d010b0b
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Revert "update TODO"
This reverts commit a054c0c20a.
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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
v3.0
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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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a054c0c20a
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update TODO
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2022-09-21 16:50:00 -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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3ba305abdb
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Update ToDo
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2022-09-21 13:30:30 -05:00 |
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eugenefischer
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3707923398
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Merge remote-tracking branch 'origin/master'
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2022-09-21 13:16:52 -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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f980722b56
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update TODO
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2022-09-21 18:09:37 +00:00 |
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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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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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b602fb02f1
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Remove obsolete comments
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2022-03-02 23:35:24 -06:00 |
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325e1ebe2b
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Add data on randomized well population behavior
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2022-03-02 23:21:56 -06:00 |
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df047267ee
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Add data on randomized well population behavior
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2022-03-02 22:54:17 -06:00 |
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03e8d31210
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Add data on randomized well population behavior
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2022-03-02 18:55:19 -06:00 |
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582dc3ef40
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Update readme
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2022-03-02 12:39:40 -06:00 |
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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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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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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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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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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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1886800873
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update readme
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2022-03-01 08:54:32 -06:00 |
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bedf0894bc
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update readme
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2022-03-01 08:45:40 -06:00 |
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2ac3451842
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update readme
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2022-03-01 08:43:48 -06:00 |
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