Add support for extra features - #1

Draft

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feat-extra-features

Commits on Sep 13, 2024

style: formatting changes
iblacksand
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1b57280

Commits on Sep 18, 2024

add documentation for extra-feature file
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e53c78f
Add support for adding extra_feature_file
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fa90597
remove extra_file check
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bad4f6d
skip feature file check
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a9927df

Commits on Sep 19, 2024

upgrade version number to 0.1.21
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67ca6c5
diagnostic printing
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05b316d
Add extra_feature_file genes to all_valid_ids
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4cad093
fix indent issue
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ed5bf9f
fix extra_file path
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b22c47e
fix function names problem
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262d580
Use df for merging extra features
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dbc1479
don't drop missing column
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1fc6f15
diagnostic logging
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cfdf84d
Remove duplicate gene pairs in extra_features
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62ba8b9
use merge instead of concat
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5691803
drop duplicates more explicitly
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28b76b3
remove extra logs
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e075c75
Add LLR calculation and plotting for extra features
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49441ac
Remove excess logging and fix llr parameters
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74448da
fix return value
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b885a86

Commits on Sep 20, 2024

Commits on Sep 25, 2024

Process extra feature file once instead of multiple times
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f6bb066

Commits on Sep 27, 2024

Commits on Sep 30, 2024

update to use latest packages
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000ae50
fix processing of extra_feature_df
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29e8c14

Commits on Oct 1, 2024

Add documentation and fix messages
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46c5fa8
add unique gene identification
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d34fc2c
add format error checking
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47dcd5e

Commits on Oct 2, 2024

save uniq_gene to pkl file in output_folder
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ca2d1f6

Commits on Oct 4, 2024

start align_file function
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4e850bc
fix rust compilation error
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799f39b

Commits on Oct 7, 2024

add code for calculating new_index for each feature file
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c67e533

Commits on Oct 8, 2024

File creation
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1af42a1
create index file
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6de0073
Remove unnecessary file read
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289185d

Commits on Oct 10, 2024

Use new feature_df creation
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a49d5ec
temporarily hard code paths
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3cab234
better error messaging
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457a0b1
add extra_feature_folder to config creation
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a4f0bc2
rename variables
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0a478d3
fix naming
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7fa7c0b
add missing imports
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ac7eb2f
fix function call
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36ca663
fix reordering dataframe
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61a80a0
logging
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8279aec
fix column names
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a177b40
fix return type
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e90285d

Commits on Oct 11, 2024

build sqlite db for extra_features
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4be7af8