Skip to content

Reorganized files #34

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

Open
wants to merge 70 commits into
base: master
Choose a base branch
from
Open

Reorganized files #34

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
70 commits
Select commit Hold shift + click to select a range
d2e1d7d
test
jimmy-penn May 15, 2024
5fa528d
Reorganize files
jimmy-penn May 15, 2024
4d4cbf6
Add medium testing
jimmy-penn May 15, 2024
1e9704f
Minor changes
jimmy-penn May 21, 2024
3c87009
Add functions to read AFs from subpopulations
jimmy-penn May 21, 2024
ecbd0c5
Add functions to calculate additional scores for subcontinental popul…
jimmy-penn May 23, 2024
19a7aa2
Add code to calculate scores for clustering African subpopulations.
jimmy-penn May 31, 2024
23ff431
Normalized newly added scores for clustering subcontinental populations.
jimmy-penn Jun 13, 2024
e849c17
Added code to save and display raw subcontinental population scores.
jimmy-penn Jun 14, 2024
a2c58e0
Fixed a bug. Removed GD4 and replaced it with a normalized score GL1.…
jimmy-penn Jun 21, 2024
0d51447
Modified code to take new list of global level reference populations
jimmy-penn Aug 27, 2024
9a6058b
Added code to calculate scores for EA subpopulations
jimmy-penn Sep 5, 2024
d7db376
Modified code to save memory space. Fixed a bug with duplicated SNP IDs.
jimmy-penn Oct 8, 2024
7db1a77
Code to check format of ancestry SNP file
jimmy-penn Oct 8, 2024
46c524d
Some minor changes
jimmy-penn Oct 8, 2024
fb38bf9
Swithed EA1 and EA3
jimmy-penn Nov 11, 2024
96b17b2
Reimplement vcf parser using htslib
jimmy-penn Nov 18, 2024
346c79b
Modified PLINK parser to allow reading a chunk of samples
jimmy-penn Nov 19, 2024
0acdea6
Optimize memory use for both VCF and PLINK input
jimmy-penn Nov 21, 2024
da47fd4
Bug fixes and minor improvements
jimmy-penn Nov 21, 2024
65d4165
Add code to calculate heterozy rate for each sample
jimmy-penn Nov 22, 2024
64752e2
Added raw Pe, Pf, Pa scores
jimmy-penn Nov 26, 2024
a19910a
Add code to take user-specified memory size, sample block size, threads
jimmy-penn Nov 27, 2024
d814ba6
Added code to assign subjects to ancestry groups
jimmy-penn Dec 23, 2024
0677785
Created test cases and modified medium testing
jimmy-penn Jan 14, 2025
9e4cdd6
README minor fix
jimmy-penn Jan 14, 2025
b950faa
Minor change of test script
jimmy-penn Jan 15, 2025
e47b2ba
Bug fixes in test script
jimmy-penn Jan 15, 2025
220506e
Added PlotGrafAnc.pl. Made some minor changes to the C++ code.
jimmy-penn Jan 17, 2025
f5a0cfe
Remomed reference populations not being used
jimmy-penn Jan 31, 2025
50dad84
Renamed GrafPop to GrafAnc
jimmy-penn Jan 31, 2025
2ccee8e
Renamed GrafPop to GrafAnc
jimmy-penn Jan 31, 2025
11c8349
Renamed GrafPop to GrafAnc
jimmy-penn Jan 31, 2025
9c7e085
Added software documentation
jimmy-penn Feb 3, 2025
912773b
Added reference pop freq file
jimmy-penn Feb 3, 2025
357d52c
Modified software documentation
jimmy-penn Feb 4, 2025
7a5562b
Added PopMeanScores.txt
jimmy-penn Feb 4, 2025
0ec8e5b
Removed the ID code Excel file
jimmy-penn Feb 4, 2025
253d3e7
Added numbers of subjects to PopMeanScores.txt
jimmy-penn Feb 5, 2025
fb97cd9
Documentation rror fixes
jimmy-penn Feb 5, 2025
bcae70f
Removed unused perl modules
jimmy-penn Feb 5, 2025
7fa99d4
Minor fix
jimmy-penn Feb 5, 2025
4e84306
Minor fix
jimmy-penn Feb 5, 2025
1fd5802
Format error fix
jimmy-penn Feb 5, 2025
6b65bf2
Format error fix
jimmy-penn Feb 5, 2025
15a32e8
Removed unused perl scripts
jimmy-penn Feb 5, 2025
ac80a61
Added one East Asia ancestry group
jimmy-penn Feb 6, 2025
a0e5f1d
Minor adjustments
jimmy-penn Feb 6, 2025
906ed51
Fixed a bug for checking PLINK set integrity. Added test cases
jimmy-penn Feb 6, 2025
f5215cb
Added prebuilt binary
jimmy-penn Feb 6, 2025
28a87c2
Moved bin directory
jimmy-penn Feb 6, 2025
d907435
Forgot to add test cases
jimmy-penn Feb 6, 2025
1e23bda
Moved the output dir
jimmy-penn Feb 6, 2025
593df6f
Removed dummy file
jimmy-penn Feb 6, 2025
51b9614
Minor fix
jimmy-penn Feb 6, 2025
cb95c05
Minor fix
jimmy-penn Feb 6, 2025
8015791
Error fixes in documentations
jimmy-penn Feb 7, 2025
72192d9
Modified code so that grafanc can be executed from 'bin' directry
jimmy-penn Feb 7, 2025
a5c81d5
Fixed array declaration problem with C99 compiler
jimmy-penn Feb 7, 2025
5439363
Bug fix for ExtractAncSnpsFromVcfGz.pl
jimmy-penn Feb 7, 2025
6dc76a1
Made grafanc callable from different directories
jimmy-penn Feb 24, 2025
8ce16c7
Updated the prebuilt binary
jimmy-penn Feb 25, 2025
b1587fa
Fixed a typo in GrafAncDocumentation.md
jimmy-penn Feb 25, 2025
c209f70
Moved Northeastern Africa from superpopulation MEN to AFR
jimmy-penn Mar 3, 2025
9c0874a
Changed ancestry group African American from AMR to AFR
jimmy-penn Mar 10, 2025
d0752a4
Added visualization tool PlotGrafAnc.py
jimmy-penn Apr 14, 2025
ce7ad85
Minor bug fixes
jimmy-penn Apr 14, 2025
bb45221
Minor changes to PlotGrafAnc.py
jimmy-penn May 9, 2025
fbf96d6
Removed # from column #SNPs in the output file to make it more machin…
jimmy-penn May 16, 2025
409bcf3
Fixed the python script. Updated the binary.
jimmy-penn May 18, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
78 changes: 0 additions & 78 deletions Build Announcements/151/README.md
View file
Open in desktop

This file was deleted.

66 changes: 0 additions & 66 deletions Build Announcements/152/README.md
View file
Open in desktop

This file was deleted.

44 changes: 0 additions & 44 deletions Frequency Project/README.md
View file
Open in desktop

This file was deleted.

Loading