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  • 4099ec2623 update ToDos master eugenefischer 2025-04-15 15:50:55 -05:00
  • 7744586e79 change frequency of garbage collection requests eugenefischer 2025-04-10 20:07:34 -05:00
  • 83eff0d1e7 remove output to stdout that was added for testing eugenefischer 2025-04-10 15:08:33 -05:00
  • d1810c453d Even more efficient graph creation (my initial scheme, but this time without accidentally changing what's in the sequence records) v4.4 eugenefischer 2025-04-10 15:03:10 -05:00
  • 187401f2d6 More efficient graph creation eugenefischer 2025-04-10 14:06:11 -05:00
  • 678ce99424 iterate over vertex wells correctly eugenefischer 2025-04-10 13:34:04 -05:00
  • c21e375303 fix concurrent modification bug eugenefischer 2025-04-10 13:33:47 -05:00
  • 57fe9c1619 Update graph modification functions to work with edges directly eugenefischer 2025-04-10 12:42:19 -05:00
  • e1888a99c6 refactor to construct the bipartite graph directly, rather than by using an adjacency matrix and a graph generator. eugenefischer 2025-04-10 11:47:15 -05:00
  • bcf5a4c749 change artifact details eugenefischer 2025-04-10 11:05:08 -05:00
  • 81d8a12765 dependency update stuff eugenefischer 2025-04-10 10:54:05 -05:00
  • b5c0568e22 Add dependencies eugenefischer 2025-04-10 10:53:42 -05:00
  • b7597cff2a update readme and add Zipf exponent option to CLI v4.3 eugenefischer 2025-04-09 16:16:46 -05:00
  • 7bbeaf7dad update readme eugenefischer 2025-04-09 14:40:49 -05:00
  • 945b967382 update readme eugenefischer 2025-04-09 14:39:46 -05:00
  • a43ee469ea implement Zipf distribution eugenefischer 2025-04-09 14:32:02 -05:00
  • 161a52aa89 update readme eugenefischer 2025-04-09 11:52:03 -05:00
  • 9b2ad9da09 update readme eugenefischer 2025-04-09 11:42:10 -05:00
  • 30a3f6e33d update citations eugenefischer 2025-04-09 11:36:06 -05:00
  • 8cc1f19da1 update links eugenefischer 2025-04-09 11:31:05 -05:00
  • 3efa5c26d8 fix index link eugenefischer 2025-04-09 11:22:13 -05:00
  • e686d4957b disable selection of the scaling integer weight MWM algorithm via the interactive interface eugenefischer 2025-04-09 11:20:52 -05:00
  • fbc0496675 update readme and default heap type eugenefischer 2025-04-09 11:18:21 -05:00
  • 0071cafbbd Rough implementation, missing final dual adjustment step, and may have other bugs as well as it does not yet output a maximum weight matching eugenefischer 2025-04-09 10:17:13 -05:00
  • 3d302cf8ad initial commit of stub of integer weight scaling algorithm eugenefischer 2025-03-27 13:42:27 -05:00
  • 5f5d77b0a4 update citations eugenefischer 2023-04-09 20:59:09 -05:00
  • af32be85ee update TODO eugenefischer 2023-04-09 20:49:39 -05:00
  • 58cdf9ae93 Lookback AA implementation, doesn't currently work eugenefischer 2023-04-09 20:45:03 -05:00
  • 202ad4c834 mention forward/reverse auction algorithms eugenefischer 2023-04-09 20:42:58 -05:00
  • 96d49d0034 clarifying comment eugenefischer 2023-04-09 19:48:43 -05:00
  • d8e5f7ece0 update todo eugenefischer 2023-04-09 13:00:41 -05:00
  • 9c81d919b4 add disclosure section eugenefischer 2023-01-18 16:28:16 -06:00
  • 70b08e7c22 Bugfixes and streamlining eugenefischer 2022-10-22 17:59:01 -05:00
  • 44158d264c Correct sequence count eugenefischer 2022-10-22 16:16:32 -05:00
  • e97c2989db Add dropout rate calculation to read-in of data from plate file (this may slow down read-in by a lot) eugenefischer 2022-10-22 16:04:41 -05:00
  • f7709ada73 Change order of metadata comments eugenefischer 2022-10-22 15:50:35 -05:00
  • 25b37eff48 renamed to MaximumIntegerWeightBipartiteAuctionMatching eugenefischer 2022-10-22 15:00:22 -05:00
  • fbbb5a8792 Update comments eugenefischer 2022-10-22 14:59:43 -05:00
  • 4b9d7f8494 Add option to select matching algorithm type, rename types in output eugenefischer 2022-10-22 14:59:24 -05:00
  • 0de12a3a12 Refactor to use selected algorithm type eugenefischer 2022-10-22 14:58:40 -05:00
  • 3c2ec9002e Add field for algorithm type, methods to set algorithm type eugenefischer 2022-10-22 14:13:31 -05:00
  • bcf3af5a83 Update algorithm type names eugenefischer 2022-10-22 14:10:00 -05:00
  • fcca22a2f0 Rename class, modify bidding to include marginal item value eugenefischer 2022-10-22 13:18:43 -05:00
  • 910de0ce9d Fix typos eugenefischer 2022-10-21 13:46:10 -05:00
  • ef349ea5f6 Correctly store matching weight eugenefischer 2022-10-14 18:44:56 -05:00
  • 174db66c46 Clean up comments eugenefischer 2022-10-14 18:31:32 -05:00
  • b3273855a6 Test simpler source/target differentiation eugenefischer 2022-10-14 18:11:21 -05:00
  • 51c1bc2551 Skip edges with zero weight eugenefischer 2022-10-14 18:09:34 -05:00
  • f7d522e95d Comment out old MWM algorithm, add auction algorithm eugenefischer 2022-10-14 17:38:07 -05:00
  • 5f0c089b0a add getter for matchingWeight eugenefischer 2022-10-14 17:37:40 -05:00
  • d3066095d9 add getter/setter for potential eugenefischer 2022-10-14 17:32:37 -05:00
  • 55a5d9a892 Making fields final eugenefischer 2022-10-14 17:32:21 -05:00
  • 49708f2f8a Initial auction algorithm implementation eugenefischer 2022-10-14 17:31:59 -05:00
  • c7934ca498 update TODO eugenefischer 2022-10-03 21:30:32 -05:00
  • 8f0ed91cb7 revert previous commit eugenefischer 2022-10-01 18:36:41 -05:00
  • 40bc2ce88d New linking test eugenefischer 2022-10-01 18:35:58 -05:00
  • a5a17d1f76 Revert previous commit v4.2 eugenefischer 2022-10-01 18:23:31 -05:00
  • 0f3ab0fdd7 Section link test eugenefischer 2022-10-01 18:22:55 -05:00
  • 01596ef43a Rename sections eugenefischer 2022-10-01 18:16:08 -05:00
  • cda25a2c62 Update performance section and TODO eugenefischer 2022-10-01 18:12:33 -05:00
  • bde6da3076 fix typo eugenefischer 2022-10-01 16:12:21 -05:00
  • 2eede214c0 fix typo eugenefischer 2022-10-01 16:11:32 -05:00
  • 98ce708825 Remove questionable claim, reorder simulation experiments eugenefischer 2022-10-01 15:46:22 -05:00
  • e7e85a4542 Comment out questionable claim eugenefischer 2022-10-01 15:44:29 -05:00
  • c0dd2d31f2 Update version number eugenefischer 2022-10-01 15:21:33 -05:00
  • cf103c5223 Add flag to enable p-value calculation eugenefischer 2022-10-01 14:36:22 -05:00
  • 26f66fe139 Remove outdated comments eugenefischer 2022-10-01 14:35:35 -05:00
  • 89295777ef Update output example eugenefischer 2022-10-01 14:30:46 -05:00
  • 99c92e6eb5 Update TODO eugenefischer 2022-10-01 14:21:23 -05:00
  • b82176517c Update TOC, command line options eugenefischer 2022-10-01 13:59:03 -05:00
  • 0657db5653 tyoo eugenefischer 2022-10-01 13:44:17 -05:00
  • 9f0ac227e2 Clarify steps and reasoning behind the algorithm eugenefischer 2022-10-01 13:43:14 -05:00
  • 54896bc47f Correct typo, remove redundant information eugenefischer 2022-10-01 13:01:44 -05:00
  • b19a4d37c2 Update readme with newer results, new menu options eugenefischer 2022-10-01 13:00:33 -05:00
  • 457d643477 Make calculation of p-values optional, defaulting to off eugenefischer 2022-09-30 03:17:58 -05:00
  • 593dd6c60f Add sample cell filename, cell sample size, and sample plate size to metadata eugenefischer 2022-09-30 02:58:15 -05:00
  • b8aeeb988f Add sequence dropout rate to metadata output eugenefischer 2022-09-30 00:33:41 -05:00
  • b9b13fb75e Rename dropout rate flag eugenefischer 2022-09-29 23:58:08 -05:00
  • 289220e0d0 Remove statements about pre-filtering types. Can add that back if I ever actually parameterize that. eugenefischer 2022-09-29 22:10:42 -05:00
  • 19badac92b Correct misstatement of filter condition in Algorithm section eugenefischer 2022-09-29 18:32:42 -05:00
  • 633334a1b8 Update Theory section, add Contents and Algorithm section. eugenefischer 2022-09-29 18:30:07 -05:00
  • e308e47578 Correct error in comments eugenefischer 2022-09-29 18:29:43 -05:00
  • 133984276f Change access modifiers and add count of wells removed to output eugenefischer 2022-09-29 15:56:19 -05:00
  • ec6713a1c0 Implement filtering for wells with anomalous read counts eugenefischer 2022-09-29 15:50:57 -05:00
  • 097590cf21 Add method to remove a well from the SequenceRecord (git committed as past self due to IDE misclick) efischer 2022-02-22 16:09:50 -06:00
  • f1e4c4f194 Remove duplicate output statements eugenefischer 2022-09-29 01:05:36 -05:00
  • b6218c3ed3 update version eugenefischer 2022-09-29 00:53:11 -05:00
  • 756e5572b9 update readme v4.1 eugenefischer 2022-09-29 00:00:19 -05:00
  • c30167d5ec Change real sequence collision so it isn't biased toward sequences in the earlier wells. eugenefischer 2022-09-28 23:15:55 -05:00
  • a19525f5bb update readme eugenefischer 2022-09-28 23:01:59 -05:00
  • e5803defa3 Bug fix, add comments eugenefischer 2022-09-28 18:09:47 -05:00
  • 34dc2a5721 Add real sequence collision rate eugenefischer 2022-09-28 17:54:55 -05:00
  • fd106a0d73 Add real sequence collision rate eugenefischer 2022-09-28 17:46:09 -05:00
  • 22faad3414 Add real sequence collision rate eugenefischer 2022-09-28 17:45:09 -05:00
  • 0b36e2b742 Rewrite countSequences to allow for collision with real sequences on misreads eugenefischer 2022-09-28 17:44:26 -05:00
  • 9dacd8cd34 Add real sequence collision rate eugenefischer 2022-09-28 17:43:21 -05:00
  • 89687fa849 Add real sequence collision rate, make fields final eugenefischer 2022-09-28 17:43:06 -05:00
  • fb443fe958 Revert "Add getCell and getRandomCell methods" eugenefischer 2022-09-28 14:36:20 -05:00
  • adebe1542e Add getCell and getRandomCell methods eugenefischer 2022-09-28 13:49:50 -05:00
  • 882fbfffc6 Purge old code eugenefischer 2022-09-28 13:40:13 -05:00