Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Implement read count model for LPhy simulation #56

Open
kche309 opened this issue Apr 18, 2024 · 0 comments
Open

Implement read count model for LPhy simulation #56

kche309 opened this issue Apr 18, 2024 · 0 comments
Labels
enhancement New feature or request

Comments

@kche309
Copy link
Collaborator

kche309 commented Apr 18, 2024

Implement a read count model for simulating nucleotide reads from phased genotype data.
@kche309 kche309 added the enhancement New feature or request label Apr 18, 2024
zjzxiaohei added a commit that referenced this issue May 13, 2024
@zjzxiaohei
Implement Read count model #56
282070a
zjzxiaohei added a commit that referenced this issue Jun 20, 2024
@zjzxiaohei
Read count model simulation and viewer for lphy #56
74a757a
zjzxiaohei added a commit that referenced this issue Jul 3, 2024
@zjzxiaohei
fix bug in read count simulator and skeleton code for beast likelihood …
81cda54 
…#56
zjzxiaohei added a commit that referenced this issue Jul 4, 2024
@zjzxiaohei
Changed multinomial distribution to Dirichlet multinomial distrbution…
9371d14 
… for readcount model #56
zjzxiaohei added a commit that referenced this issue Jul 19, 2024
@zjzxiaohei
Remove excess code in CoverageModel #56
26de2ab
zjzxiaohei added a commit that referenced this issue Jul 19, 2024
@zjzxiaohei
working on calculating the likelihood of Readcount Model #56
cc77288
zjzxiaohei added a commit that referenced this issue Jul 19, 2024
@zjzxiaohei
calculate the likelihood of read count model #56
d32a7b0
zjzxiaohei added a commit that referenced this issue Jul 28, 2024
@zjzxiaohei
Delete some comments #56
c8352ea
zjzxiaohei added a commit that referenced this issue Jul 28, 2024
@zjzxiaohei
Add a method to set value of the object #56
0c23aa4
zjzxiaohei added a commit that referenced this issue Jul 28, 2024
@zjzxiaohei
Fix a bug about parameter "s" #56
87158c4
zjzxiaohei added a commit that referenced this issue Jul 29, 2024
@zjzxiaohei
Fix a bug about parameter "s" #56
1e49255
zjzxiaohei added a commit that referenced this issue Jul 29, 2024
@zjzxiaohei
Tidy up the script #56
217bfba
zjzxiaohei added a commit that referenced this issue Jul 29, 2024
@zjzxiaohei
Try to do a unit test for readCountModel #56
b80f586
zjzxiaohei added a commit that referenced this issue Jul 29, 2024
@zjzxiaohei
Override the setParam method #56
a259164
zjzxiaohei added a commit that referenced this issue Jul 29, 2024
@zjzxiaohei
Override the setParam method #56
5517f83
zjzxiaohei added a commit that referenced this issue Jul 29, 2024
@zjzxiaohei
Override the setParam method #56
968ed13
zjzxiaohei added a commit that referenced this issue Jul 29, 2024
@zjzxiaohei
Restructure the script with a data and model block #56
0bf3d34
zjzxiaohei added a commit that referenced this issue Aug 1, 2024
@zjzxiaohei
Fix a bug of setReadCounts method #56
1abd797
zjzxiaohei added a commit that referenced this issue Aug 3, 2024
@zjzxiaohei
Tidy up the code of ReadCountModel #56
8e29f37
zjzxiaohei added a commit that referenced this issue Aug 3, 2024
@zjzxiaohei
Unit test for ReadCountModel #56
a682016
walterxie added a commit that referenced this issue Aug 5, 2024
@walterxie
fix build #56
29f1f6b
walterxie added a commit that referenced this issue Aug 5, 2024
@walterxie
add release for beast module, fix some unit tests, and one still has …
4015472 
…a problem #56
walterxie added a commit that referenced this issue Aug 5, 2024
@walterxie
add release for lphy, studio, lphybeast part #56
86a9573
zjzxiaohei added a commit that referenced this issue Aug 6, 2024
@zjzxiaohei
Upload two files for unit test #56
ce88370
zjzxiaohei added a commit that referenced this issue Aug 9, 2024
@zjzxiaohei
Use binomial distribution instead of multinomial distribution in Ploi…
8ca929e 
…dyModel #56
zjzxiaohei added a commit that referenced this issue Sep 3, 2024
@zjzxiaohei
Modify the ReadCountModel to use log space and do unit test #56
60e42bb
zjzxiaohei added a commit that referenced this issue Sep 3, 2024
@zjzxiaohei
Add readcount and readcountmodel #56
c13754b
zjzxiaohei added a commit that referenced this issue Sep 3, 2024
@zjzxiaohei
Use longer sequence #56
2f85425
zjzxiaohei added a commit that referenced this issue Sep 3, 2024
@zjzxiaohei
ReadCountModel xml #56
738124a
zjzxiaohei added a commit that referenced this issue Sep 3, 2024
@zjzxiaohei
Test Gamma of large number #56
6263b98
zjzxiaohei added a commit that referenced this issue Sep 3, 2024
@zjzxiaohei
Use normal distribution for parameter s #56
b93c323
zjzxiaohei added a commit that referenced this issue Sep 12, 2024
@zjzxiaohei
Rename ReadCountModel.class to LikelihoodReadCountModel.class in Beast …
7a0b39f 
…#56
zjzxiaohei added a commit that referenced this issue Sep 25, 2024
@zjzxiaohei
Add GeneratorInfo #56
3140c59
zjzxiaohei added a commit that referenced this issue Oct 14, 2024
@zjzxiaohei
Fix 2 bugs about parameter w and epsilon #56
093f420
zjzxiaohei added a commit that referenced this issue Oct 14, 2024
@zjzxiaohei
Just change some values of parameters #56
29f8739
zjzxiaohei added a commit that referenced this issue Oct 14, 2024
@zjzxiaohei
Change coverage and alpha to Integer2DMatrix #56
03a9cce
zjzxiaohei added a commit that referenced this issue Oct 14, 2024
@zjzxiaohei
Exclude PloidyModel.class, CoverageModel.class and Integer2DMatrix.cl…
a279552 
…ass #56
zjzxiaohei added a commit that referenced this issue Oct 14, 2024
@zjzxiaohei
Change expected value #56
44e35f8
zjzxiaohei added a commit that referenced this issue Oct 20, 2024
@zjzxiaohei
Add a Viewer of Integer2DMatrix #56
536738d
zjzxiaohei added a commit that referenced this issue Oct 20, 2024
@zjzxiaohei
LPhy to BEAST(readCountModel) #56
3d18a0d
zjzxiaohei added a commit that referenced this issue Oct 28, 2024
@zjzxiaohei
Fix a bug(getBEASTObject for RealParam) #56
2ec6f5b
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement New feature or request
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@kche309