eugenefischer
|
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)
|
2022-09-26 23:03:23 -05:00 |
|
eugenefischer
|
13a1af1f71
|
placeholder values until CLI is updated to support read depth simulation
|
2022-09-26 19:43:29 -05:00 |
|
eugenefischer
|
199c81f983
|
Implement read count for vertices
|
2022-09-26 19:42:19 -05:00 |
|
eugenefischer
|
19a2a35f07
|
Refactor plate assay methods to use maps passed as parameters rather than returning maps
|
2022-09-26 17:00:25 -05:00 |
|
eugenefischer
|
36c628cde5
|
Add code to simulate read depth
|
2022-09-26 16:52:56 -05:00 |
|
eugenefischer
|
1ddac63b0a
|
Add exception handling
|
2022-09-26 14:28:35 -05:00 |
|
eugenefischer
|
e795b4cdd0
|
Add read depth option to interface
|
2022-09-26 14:25:47 -05:00 |
|
eugenefischer
|
60cf6775c2
|
notes toward command line read depth option
|
2022-09-26 14:25:30 -05:00 |
|
eugenefischer
|
8a8c89c9ba
|
revert options menu
|
2022-09-26 14:24:58 -05:00 |
|
eugenefischer
|
86371668d5
|
Add menu option to activate simulation of read depth and sequence read errors
|
2022-09-26 13:47:19 -05:00 |
|
eugenefischer
|
d81ab25a68
|
Comment: need to update this when read count is implemented
|
2022-09-26 13:46:53 -05:00 |
|
eugenefischer
|
02c8e6aacb
|
Refactor sequences to be strings instead of integers, to make simulating read errors easier
|
2022-09-26 13:37:48 -05:00 |
|
eugenefischer
|
f84dfb2b4b
|
Method stub for simulating read depth
|
2022-09-26 00:43:13 -05:00 |
|
eugenefischer
|
184278b72e
|
Add fields for simulating read depth. Also a priority queue for lookback auctions
|
2022-09-26 00:42:55 -05:00 |
|
eugenefischer
|
489369f533
|
Add flag to simulate read depth
|
2022-09-26 00:42:23 -05:00 |
|
eugenefischer
|
fbee591273
|
Change indentation
|
2022-09-25 22:36:02 -05:00 |
|
eugenefischer
|
603a999b59
|
Update readme
|
2022-09-25 22:35:52 -05:00 |
|
eugenefischer
|
c3df4b12ab
|
Update readme with read depth TODO
|
2022-09-25 21:50:59 -05:00 |
|
eugenefischer
|
d1a56c3578
|
Hand-merge of some things from Dev_Vertex branch that didn't make it in for some reason
|
2022-09-25 19:07:25 -05:00 |
|
eugenefischer
|
16daf02dd6
|
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
|
2022-09-25 18:33:26 -05:00 |
|
eugenefischer
|
04a077da2e
|
update Readme
|
2022-09-25 18:24:12 -05:00 |
|
eugenefischer
|
740835f814
|
fix typo
|
2022-09-25 17:47:07 -05:00 |
|
eugenefischer
|
8a77d53f1f
|
Output sequence counts before and after pre-filtering (currently pre-filtering only sequences present in all wells)
|
2022-09-25 17:20:50 -05:00 |
|
eugenefischer
|
58fa140ee5
|
add comments
|
2022-09-25 16:10:17 -05:00 |
|
eugenefischer
|
475bbf3107
|
Sort vertex lists by vertex label before making adjacency matrix
|
2022-09-25 15:54:28 -05:00 |
|
eugenefischer
|
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)
|
2022-09-25 15:19:56 -05:00 |
|
eugenefischer
|
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)
|
2022-09-25 15:06:46 -05:00 |
|
eugenefischer
|
1971a96467
|
Remove pre-filtering of singleton and saturating sequences
|
2022-09-25 14:55:43 -05:00 |
|
eugenefischer
|
e699795521
|
Revert "by-hand merge of needed code from custom vertex branch"
This reverts commit 29b844afd2.
|
2022-09-25 14:34:31 -05:00 |
|
eugenefischer
|
bd6d010b0b
|
Revert "update TODO"
This reverts commit a054c0c20a.
|
2022-09-25 14:34:31 -05:00 |
|
eugenefischer
|
61d1eb3eb1
|
Revert "Reword output message"
This reverts commit 63317f2aa0.
|
2022-09-25 14:34:31 -05:00 |
|
eugenefischer
|
cb41b45204
|
Revert "Reword option menu item"
This reverts commit 06e72314b0.
|
2022-09-25 14:34:31 -05:00 |
|
eugenefischer
|
a84d2e1bfe
|
Revert "Add comment on map data encodng"
This reverts commit 73c83bf35d.
|
2022-09-25 14:34:31 -05:00 |
|
eugenefischer
|
7b61d2c0d7
|
Revert "update version number"
This reverts commit e4e5a1f979.
|
2022-09-25 14:34:31 -05:00 |
|
eugenefischer
|
56454417c0
|
Revert "Restore pre-filtering of singleton and saturating sequences"
This reverts commit 5c03909a11.
|
2022-09-25 14:34:31 -05:00 |
|
eugenefischer
|
8ee1c5903e
|
Merge branch 'master' into Dev_Vertex
# Conflicts:
# src/main/java/GraphMLFileReader.java
# src/main/java/InteractiveInterface.java
# src/main/java/Simulator.java
|
2022-09-25 14:18:56 -05:00 |
|
eugenefischer
|
5c03909a11
|
Restore pre-filtering of singleton and saturating sequences
|
2022-09-22 01:39:13 -05:00 |
|
eugenefischer
|
e4e5a1f979
|
update version number
v3.0
|
2022-09-22 00:00:02 -05:00 |
|
eugenefischer
|
73c83bf35d
|
Add comment on map data encodng
|
2022-09-21 21:46:00 -05:00 |
|
eugenefischer
|
06e72314b0
|
Reword option menu item
|
2022-09-21 21:43:47 -05:00 |
|
eugenefischer
|
63317f2aa0
|
Reword output message
|
2022-09-21 18:08:52 -05:00 |
|
eugenefischer
|
a054c0c20a
|
update TODO
|
2022-09-21 16:50:00 -05:00 |
|
eugenefischer
|
29b844afd2
|
by-hand merge of needed code from custom vertex branch
|
2022-09-21 16:48:26 -05:00 |
|
eugenefischer
|
dea4972927
|
remove prefiltering of singletons and saturating sequences
|
2022-09-21 16:09:08 -05:00 |
|
eugenefischer
|
9ae38bf247
|
Fix bug in correct match counter
|
2022-09-21 15:59:23 -05:00 |
|
eugenefischer
|
3ba305abdb
|
Update ToDo
|
2022-09-21 13:30:30 -05:00 |
|
eugenefischer
|
3707923398
|
Merge remote-tracking branch 'origin/master'
|
2022-09-21 13:16:52 -05:00 |
|
eugenefischer
|
cf771ce574
|
parameterized sequence indices
|
2022-09-21 13:15:49 -05:00 |
|
|
|
f980722b56
|
update TODO
|
2022-09-21 18:09:37 +00:00 |
|
|
|
1df86f01df
|
parameterized sequence indices
|
2022-03-05 12:03:31 -06:00 |
|
