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Adapt hl.de_novo function #760

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f24e6a5
Add function to compute post probability of de novos
KoalaQin Jan 21, 2025
3f3f8e3
confidence and fail check function
KoalaQin Jan 24, 2025
e681bdc
Modify de novo function
KoalaQin Jan 28, 2025
4ee8cdc
black formatting
KoalaQin Jan 29, 2025
376811d
Reformat docstring
KoalaQin Jan 29, 2025
f80698c
Change the citation
KoalaQin Jan 29, 2025
ddf3811
Apply suggestions from code review
KoalaQin Jan 30, 2025
b5fc1b7
Transpose the thresholds table
KoalaQin Jan 30, 2025
05a4320
merge origin changes
KoalaQin Jan 30, 2025
b565fa2
Add a call_de_novo function
KoalaQin Jan 31, 2025
2f11811
Formatting
KoalaQin Jan 31, 2025
f4dfe32
isort
KoalaQin Jan 31, 2025
dce95f0
Add test module for de novo functions
KoalaQin Feb 3, 2025
7ccda17
small formatting
KoalaQin Feb 3, 2025
e9d49d4
black formatting
KoalaQin Feb 3, 2025
ef6dbe1
Black
KoalaQin Feb 3, 2025
0a5616d
isort
KoalaQin Feb 3, 2025
4376c66
Add missing docstring and notes
KoalaQin Feb 3, 2025
6bfd82e
formatting
KoalaQin Feb 3, 2025
3d977d7
Apply suggestions from code review
KoalaQin Feb 5, 2025
7252583
Reformat docstring and move helper functions
KoalaQin Feb 5, 2025
90ab407
Correct the confidence errors
KoalaQin Feb 5, 2025
2816f9c
Move is_de_novo
KoalaQin Feb 5, 2025
50f4745
reST hyperlink format in docstring
KoalaQin Feb 5, 2025
bffe574
Add test
KoalaQin Feb 6, 2025
f9a625b
Black
KoalaQin Feb 6, 2025
46538d2
remove imports
KoalaQin Feb 6, 2025
d7d69b5
docstring typo
KoalaQin Feb 6, 2025
9d37bcb
Apply suggestions from code review
KoalaQin Feb 7, 2025
f70125d
Docstring changes
KoalaQin Feb 7, 2025
fcfa796
Merge suggestions
KoalaQin Feb 7, 2025
a387d19
A small change
KoalaQin Feb 7, 2025
f45bc3c
Add error case
KoalaQin Feb 7, 2025
9c36896
Add suggested test cases
KoalaQin Feb 7, 2025
768d9f4
Black
KoalaQin Feb 7, 2025
c2050d0
extra space removal
KoalaQin Feb 7, 2025
2742e26
Add warning block back
KoalaQin Feb 7, 2025
285865c
Change wording
KoalaQin Feb 7, 2025
ace2d37
Apply suggestions from code review
KoalaQin Feb 8, 2025
49f6249
Address review comments
KoalaQin Feb 8, 2025
457cd9a
Black
KoalaQin Feb 8, 2025
3571265
Change indel HIGH code
KoalaQin Feb 8, 2025
9b1515b
typo
KoalaQin Feb 8, 2025
b899e7b
Remove extra
KoalaQin Feb 9, 2025
5631c62
Adjust table
KoalaQin Feb 9, 2025
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