efischer/BiGpairSEQ
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Commit Graph

  • a88cfb8b0d Add read counts for individual wells to graphml output eugenefischer 2022-09-28 13:38:38 -05:00
  • deed98e79d Bugfix eugenefischer 2022-09-28 12:58:14 -05:00
  • 1a35600f50 Add method to get read count from individual wells eugenefischer 2022-09-28 12:57:45 -05:00
  • 856063529b Read depth simulation is now compatible with plate caching eugenefischer 2022-09-28 12:47:00 -05:00
  • b7c86f20b3 Add read depth attributes to graphml output v4.0 eugenefischer 2022-09-28 03:01:52 -05:00
  • 3a47efd361 Update TODO eugenefischer 2022-09-28 03:01:03 -05:00
  • 58bb04c431 Remove redundant toString() calls eugenefischer 2022-09-28 02:08:17 -05:00
  • 610da68262 Refactor Vertex class to use SequenceRecords eugenefischer 2022-09-28 00:58:44 -05:00
  • 9973473cc6 Make serializable and implement getWellOccupancies method eugenefischer 2022-09-28 00:58:02 -05:00
  • 8781afd74c Reorder conditional eugenefischer 2022-09-28 00:57:06 -05:00
  • 88b6c79caa Refactor to simplify graph creation code eugenefischer 2022-09-28 00:07:59 -05:00
  • 35a519d499 update TODO eugenefischer 2022-09-27 22:20:57 -05:00
  • 5bd1e568a6 update TODO eugenefischer 2022-09-27 15:08:16 -05:00
  • 4ad1979c18 Add read depth simulation options to CLI eugenefischer 2022-09-27 15:05:50 -05:00
  • 423c9d5c93 Add read depth simulation options to CLI eugenefischer 2022-09-27 14:35:55 -05:00
  • 7c3c95ab4b update TODO in readme eugenefischer 2022-09-27 14:11:21 -05:00
  • d71a99555c clean up metadata eugenefischer 2022-09-27 12:15:12 -05:00
  • 2bf2a9f5f7 Add comments eugenefischer 2022-09-27 11:51:51 -05:00
  • 810abdb705 Add read depth parameters to output metadata eugenefischer 2022-09-27 11:13:12 -05:00
  • f7b3c133bf Add filtering based on occupancy/read count discrepancy eugenefischer 2022-09-26 23:39:18 -05:00
  • 14fcfe1ff3 spacing eugenefischer 2022-09-26 23:38:56 -05:00
  • 70fec95a00 Bug fix eugenefischer 2022-09-26 23:17:18 -05:00
  • 077af3b46e Clear plate in memory when simulating read depth eugenefischer 2022-09-26 23:17:10 -05:00
  • db99c74810 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) eugenefischer 2022-09-26 23:03:23 -05:00
  • 13a1af1f71 placeholder values until CLI is updated to support read depth simulation eugenefischer 2022-09-26 19:43:29 -05:00
  • 199c81f983 Implement read count for vertices eugenefischer 2022-09-26 19:42:19 -05:00
  • 19a2a35f07 Refactor plate assay methods to use maps passed as parameters rather than returning maps eugenefischer 2022-09-26 17:00:25 -05:00
  • 36c628cde5 Add code to simulate read depth eugenefischer 2022-09-26 16:52:56 -05:00
  • 1ddac63b0a Add exception handling eugenefischer 2022-09-26 14:28:35 -05:00
  • e795b4cdd0 Add read depth option to interface eugenefischer 2022-09-26 14:25:47 -05:00
  • 60cf6775c2 notes toward command line read depth option eugenefischer 2022-09-26 14:25:30 -05:00
  • 8a8c89c9ba revert options menu eugenefischer 2022-09-26 14:24:58 -05:00
  • 86371668d5 Add menu option to activate simulation of read depth and sequence read errors eugenefischer 2022-09-26 13:47:19 -05:00
  • d81ab25a68 Comment: need to update this when read count is implemented eugenefischer 2022-09-26 13:46:53 -05:00
  • 02c8e6aacb Refactor sequences to be strings instead of integers, to make simulating read errors easier eugenefischer 2022-09-26 13:37:48 -05:00
  • f84dfb2b4b Method stub for simulating read depth eugenefischer 2022-09-26 00:43:13 -05:00
  • 184278b72e Add fields for simulating read depth. Also a priority queue for lookback auctions eugenefischer 2022-09-26 00:42:55 -05:00
  • 489369f533 Add flag to simulate read depth eugenefischer 2022-09-26 00:42:23 -05:00
  • fbee591273 Change indentation eugenefischer 2022-09-25 22:36:02 -05:00
  • 603a999b59 Update readme eugenefischer 2022-09-25 22:35:52 -05:00
  • c3df4b12ab Update readme with read depth TODO eugenefischer 2022-09-25 21:50:59 -05:00
  • d1a56c3578 Hand-merge of some things from Dev_Vertex branch that didn't make it in for some reason eugenefischer 2022-09-25 19:07:25 -05:00
  • 16daf02dd6 Merge branch 'Dev_Vertex' eugenefischer 2022-09-25 18:33:26 -05:00
  • 04a077da2e update Readme eugenefischer 2022-09-25 18:24:12 -05:00
  • 740835f814 fix typo eugenefischer 2022-09-25 17:47:07 -05:00
  • 8a77d53f1f Output sequence counts before and after pre-filtering (currently pre-filtering only sequences present in all wells) eugenefischer 2022-09-25 17:20:50 -05:00
  • 58fa140ee5 add comments eugenefischer 2022-09-25 16:10:17 -05:00
  • 475bbf3107 Sort vertex lists by vertex label before making adjacency matrix eugenefischer 2022-09-25 15:54:28 -05:00
  • 4f2fa4cbbe 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) eugenefischer 2022-09-25 15:19:56 -05:00
  • 58d418e44b 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) eugenefischer 2022-09-25 15:06:46 -05:00
  • 1971a96467 Remove pre-filtering of singleton and saturating sequences eugenefischer 2022-09-25 14:55:43 -05:00
  • e699795521 Revert "by-hand merge of needed code from custom vertex branch" eugenefischer 2022-09-25 14:34:31 -05:00
  • bd6d010b0b Revert "update TODO" eugenefischer 2022-09-25 14:34:31 -05:00
  • 61d1eb3eb1 Revert "Reword output message" eugenefischer 2022-09-25 14:34:31 -05:00
  • cb41b45204 Revert "Reword option menu item" eugenefischer 2022-09-25 14:34:31 -05:00
  • a84d2e1bfe Revert "Add comment on map data encodng" eugenefischer 2022-09-25 14:34:31 -05:00
  • 7b61d2c0d7 Revert "update version number" eugenefischer 2022-09-25 14:34:31 -05:00
  • 56454417c0 Revert "Restore pre-filtering of singleton and saturating sequences" eugenefischer 2022-09-25 14:34:31 -05:00
  • 8ee1c5903e Merge branch 'master' into Dev_Vertex eugenefischer 2022-09-25 14:18:56 -05:00
  • 5c03909a11 Restore pre-filtering of singleton and saturating sequences eugenefischer 2022-09-22 01:39:13 -05:00
  • e4e5a1f979 update version number v3.0 eugenefischer 2022-09-22 00:00:02 -05:00
  • 73c83bf35d Add comment on map data encodng eugenefischer 2022-09-21 21:46:00 -05:00
  • 06e72314b0 Reword option menu item eugenefischer 2022-09-21 21:43:47 -05:00
  • 63317f2aa0 Reword output message eugenefischer 2022-09-21 18:08:52 -05:00
  • a054c0c20a update TODO eugenefischer 2022-09-21 16:50:00 -05:00
  • 29b844afd2 by-hand merge of needed code from custom vertex branch eugenefischer 2022-09-21 16:48:26 -05:00
  • dea4972927 remove prefiltering of singletons and saturating sequences eugenefischer 2022-09-21 16:09:08 -05:00
  • 9ae38bf247 Fix bug in correct match counter eugenefischer 2022-09-21 15:59:23 -05:00
  • 3ba305abdb Update ToDo eugenefischer 2022-09-21 13:30:30 -05:00
  • 3707923398 Merge remote-tracking branch 'origin/master' eugenefischer 2022-09-21 13:16:52 -05:00
  • cf771ce574 parameterized sequence indices eugenefischer 2022-09-21 13:15:49 -05:00
  • f980722b56 update TODO efischer 2022-09-21 18:09:37 +00:00
  • 1df86f01df parameterized sequence indices efischer 2022-03-05 12:02:58 -06:00
  • 96ba57d653 Remove singleton sequences from wells in initial filtering efischer 2022-03-04 16:14:17 -06:00
  • b602fb02f1 Remove obsolete comments efischer 2022-03-02 23:35:24 -06:00
  • 325e1ebe2b Add data on randomized well population behavior efischer 2022-03-02 23:21:56 -06:00
  • df047267ee Add data on randomized well population behavior efischer 2022-03-02 22:54:17 -06:00
  • 03e8d31210 Add data on randomized well population behavior efischer 2022-03-02 18:55:19 -06:00
  • 582dc3ef40 Update readme efischer 2022-03-02 12:39:40 -06:00
  • 4c872ed48e Add optional stdout print flags efischer 2022-03-01 15:27:04 -06:00
  • 3fc39302c7 Add detail to error message efischer 2022-03-01 15:24:14 -06:00
  • 578bdc0fbf clarify help menu text efischer 2022-03-01 15:08:43 -06:00
  • 8275cf7740 Check for finite pairing error rate efischer 2022-03-01 09:01:53 -06:00
  • 64209691f0 Check for finite pairing error rate efischer 2022-03-01 09:00:58 -06:00
  • 1886800873 update readme efischer 2022-03-01 08:54:32 -06:00
  • bedf0894bc update readme efischer 2022-03-01 08:45:40 -06:00
  • 2ac3451842 update readme efischer 2022-03-01 08:43:48 -06:00
  • 67ec3f3764 update readme efischer 2022-03-01 08:43:18 -06:00
  • b5a8b7e2d5 update readme efischer 2022-03-01 08:41:57 -06:00
  • 9fb3095f0f Clarify help text efischer 2022-03-01 08:40:34 -06:00
  • 25acf920c2 Add version information efischer 2022-03-01 08:34:35 -06:00
  • f301327693 Update readme with -graphml flag efischer 2022-03-01 08:24:43 -06:00
  • e04d2d6777 Fix typos in help menu efischer 2022-03-01 08:16:06 -06:00
  • 3e41afaa64 bugfix efischer 2022-02-27 19:08:29 -06:00
  • bc5d67680d Add flag to print metadata to stdout efischer 2022-02-27 17:36:23 -06:00
  • f2347e8fc2 check verbose flag efischer 2022-02-27 17:35:50 -06:00
  • c8364d8a6e check verbose flag efischer 2022-02-27 17:34:20 -06:00
  • 6f5afbc6ec Update readme with CLI arguments v2.0 efischer 2022-02-27 17:01:12 -06:00
  • fb4d22e7a4 Update readme with CLI arguments efischer 2022-02-27 17:00:54 -06:00
  • e10350c214 Update readme with CLI arguments efischer 2022-02-27 16:56:58 -06:00