 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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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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35a519d499
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update TODO
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2022-09-27 22:20:57 -05:00 |
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eugenefischer
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5bd1e568a6
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update TODO
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2022-09-27 15:08:16 -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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7c3c95ab4b
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update TODO in readme
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2022-09-27 14:11:21 -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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eugenefischer
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70fec95a00
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Bug fix
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2022-09-26 23:17:18 -05:00 |
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eugenefischer
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077af3b46e
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Clear plate in memory when simulating read depth
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2022-09-26 23:17:10 -05:00 |
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eugenefischer
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db99c74810
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Rework read depth simulation to allow edge weight calculations to work as expected. (This changes sample plate in memory, so caching the sample plate is incompatible)
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2022-09-26 23:03:23 -05:00 |
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eugenefischer
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13a1af1f71
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placeholder values until CLI is updated to support read depth simulation
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2022-09-26 19:43:29 -05:00 |
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eugenefischer
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199c81f983
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Implement read count for vertices
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2022-09-26 19:42:19 -05:00 |
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eugenefischer
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19a2a35f07
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Refactor plate assay methods to use maps passed as parameters rather than returning maps
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2022-09-26 17:00:25 -05:00 |
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eugenefischer
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36c628cde5
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Add code to simulate read depth
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2022-09-26 16:52:56 -05:00 |
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eugenefischer
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1ddac63b0a
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Add exception handling
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2022-09-26 14:28:35 -05:00 |
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eugenefischer
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e795b4cdd0
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Add read depth option to interface
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2022-09-26 14:25:47 -05:00 |
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eugenefischer
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60cf6775c2
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notes toward command line read depth option
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2022-09-26 14:25:30 -05:00 |
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eugenefischer
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8a8c89c9ba
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revert options menu
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2022-09-26 14:24:58 -05:00 |
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eugenefischer
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86371668d5
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Add menu option to activate simulation of read depth and sequence read errors
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2022-09-26 13:47:19 -05:00 |
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eugenefischer
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d81ab25a68
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Comment: need to update this when read count is implemented
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2022-09-26 13:46:53 -05:00 |
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eugenefischer
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02c8e6aacb
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Refactor sequences to be strings instead of integers, to make simulating read errors easier
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2022-09-26 13:37:48 -05:00 |
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eugenefischer
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f84dfb2b4b
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Method stub for simulating read depth
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2022-09-26 00:43:13 -05:00 |
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eugenefischer
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184278b72e
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Add fields for simulating read depth. Also a priority queue for lookback auctions
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2022-09-26 00:42:55 -05:00 |
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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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