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Interval check for re-defined microhaps #112

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merged 5 commits into from
Feb 28, 2023
Merged

Interval check for re-defined microhaps #112

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6224d02
Interval check for redundant MH names
Feb 27, 2023
f7bf25c
Restore Sun 2020
Feb 27, 2023
7e3638a
Frequencies and rebuild
Feb 27, 2023
11d5dee
New build, test suite update
Feb 27, 2023
1ced747
Update standardize_id function to make sure that queries are either m…
Feb 28, 2023
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1 change: 1 addition & 0 deletions dbbuild/README.md
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Expand Up @@ -179,6 +179,7 @@ They can be installed using pip and/or conda.
- ucsc-liftover
- selenium
- geckodriver
- intervaltree
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New dependency for dbbuild.


### Databases

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95 changes: 72 additions & 23 deletions dbbuild/build-summary.txt
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4 changes: 3 additions & 1 deletion dbbuild/build.py
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Expand Up @@ -2,10 +2,12 @@

from lib import SourceIndex

index = SourceIndex("sources", "databases/dbSNP", "databases")
index = SourceIndex("sources", "databases/dbSNP", "databases", exclude=["Auton2015"])
index.interval_check()
index.update_marker_names()
index.markers.to_csv("marker.csv", index=False)
index.indels.to_csv("indels.csv", index=False)
index.frequencies.to_csv("frequency.csv", index=False, float_format="%.5f")
index.populations.to_csv("population.csv", index=False)
index.merges.to_csv("merged.csv", index=False)
print(index)