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Changes to TRTools #1

Merged
merged 138 commits into from
Mar 8, 2023
Merged

Changes to TRTools #1

merged 138 commits into from
Mar 8, 2023

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aarushi03
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gymreklab and others added 30 commits February 23, 2021 15:40
@gymreklab
statstr quit if no samples from the samples list in the target vcf
0959f76
@gymreklab
change msg to warning for errors so they show up
28d3e09
@Kulivox
added new field to TRRecord which holds position of full alleles
e9e9ac4
@Kulivox
HipSTR harmonization sets TRRecord position to position of record wit…
0c7b6e6 
…hout flanking bp at the start
@Kulivox
Added correct types to mergeutils.py functions
927f1f3
@Kulivox
Added multipledispatch lib to requirements
9ad411a
@Kulivox
Fixed problems revealed by static type analysis and added functions t…
786bfee 
…hat use multiple dispatch
@Kulivox
Fixed bug in compareSTR.py
0a52fd9
@Kulivox
Added utility function to tr_harmonizer.py
a8cf756
@Kulivox
Implemented improved record comparison, records are now harmonized be…
e2db6cf 
…fore the ability to compare them is calculated, fixes HipSTR issue
@Kulivox
updated RELEASE_NOTES.rst
d098089
@Kulivox
added utility function to mergeutils.py
9cec45a
@Kulivox
Removed multiple dispatch and created new function for choosing which…
1db076d 
… harmonized record should be skipped
@Kulivox
Added type annotations to mergeSTR.py
ef84886
@Kulivox
Added annotations that were revealed to be missing by mypy
f6a6c76
@Kulivox
mergeSTR.py now uses harmonized position to figure out which records …
b108664 
…can be merged
@Kulivox
added tests for additions to TRHarmonizer
51401ea
@Kulivox
removed duplicated function in mergeutils.py
924092a
@Kulivox
added test for getMinHarmonizedRecords from mergeutils
9be775c
@Kulivox
updated compareSTR.py to use harmonized values UpdateComparisonResults
c481ac7
@Kulivox
added tests for comparison of harmonized HipSTR records
482407b
@Kulivox
removed incomplete test
6f33b7d
@Kulivox
added docstring for new function in mergeutils.py
e230a56
@Kulivox
Updated release notes to better describe changes
a4cf7ce
@LiterallyUniqueLogin
Update docs, remove extra copies of VCFs
43b5aff
@LiterallyUniqueLogin
More doc cleanup
a77ed17
@Kulivox
added new test cases to test_mergeutils.py
9956a7d
@Kulivox
Added new test cases to test_compareSTR.py
834e689
@Kulivox
removed HarmonizeRecords function, reordered conditions in main loop …
6730e6a 
…of compareSTR.py to correctly handle None Records from getNextRecords
@LiterallyUniqueLogin
Merge pull request #147 from Kulivox/hipstr-flanking-bp-pos-fix
5f7fc5c 
Hipstr flanking bp pos fix
LiterallyUniqueLogin and others added 29 commits September 1, 2022 14:08
@LiterallyUniqueLogin
Bump to 4.2.0
1f8ac36
@LiterallyUniqueLogin
Merge pull request #168 from gymreklab/develop
1e84ea9 
Merge develop to master
@LiterallyUniqueLogin
Publishing clarifications
242be0d
@LiterallyUniqueLogin
Fix indentation issue in Beagle docs
4f4191c
@LiterallyUniqueLogin
Fix cmdline test bug during bioconda build
5b5c929
@LiterallyUniqueLogin
Version bump
0ef9409
@LiterallyUniqueLogin
Add counting number of alleles to statSTR
b3548c3
@LiterallyUniqueLogin
Fix flag name
385630c
@LiterallyUniqueLogin
Fix error formatting
5f45948
@LiterallyUniqueLogin
Merge pull request #170 from gymreklab/statstr_num_alleles
757b955 
Add counting number of alleles to statSTR
@LiterallyUniqueLogin
Address Melissa's comments
b8c0090
@LiterallyUniqueLogin
Merge pull request #169 from gymreklab/develop
cf3419f 
Fix cmdline test bug during bioconda build. Also clarify Publishing docs
@LiterallyUniqueLogin
Doc clarification around how to use Beagle
2c07013
@LiterallyUniqueLogin
Doc clarification around how to use Beagle
16b17cd
@gymreklab
Merge pull request #173 from gymreklab/develop
8a3cb77 
Small update to the docs about Beagle
@LiterallyUniqueLogin
Start adding support for associaTR.
386cae2
@LiterallyUniqueLogin
First pass at getting plotting stats working again
4298fa8
@LiterallyUniqueLogin
AssociaTR first pass! Now need to test it all, write tests and docs
bfb453e
@LiterallyUniqueLogin
AssociaTR is now passing the first tests!
4eaba34
@LiterallyUniqueLogin
Most of the associaTR tests are done and pass
6d9037f
@LiterallyUniqueLogin
associaTR dosage tests pass
b601cb0
@LiterallyUniqueLogin
Got associaTR mostly fully tested
d3970db
@LiterallyUniqueLogin
A few small changes to associaTR, and wrote the associaTR docs
0d15c05
@LiterallyUniqueLogin
Bump version
09c4e31
@LiterallyUniqueLogin
Merge pull request #174 from gymreklab/associaTR
50ae86c 
AssociaTR
@LiterallyUniqueLogin
Fix a docs bug
bf75f5e
@LiterallyUniqueLogin
Fix a bug in QCstr relating to outdated numpy code. Add command line …
9fedb40 
…tests for associaTR. Add version flag to associaTR.
@LiterallyUniqueLogin
Bump version
72c8c65
@gymreklab
Merge pull request #176 from gymreklab/v5.0.1
7ea6ff4 
Fix a bug in qcSTR
@aarushi03 aarushi03 merged commit 4ebeb24 into aarushi03:master Mar 8, 2023
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5 participants
@aarushi03 @gymreklab @Kulivox @LiterallyUniqueLogin @yli091230