Interval check for re-defined microhaps (#112)

bioforensics · Feb 28, 2023 · e9d5f63 · e9d5f63
1 parent 7ad401e
commit e9d5f63
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diff --git a/dbbuild/README.md b/dbbuild/README.md
@@ -179,6 +179,7 @@ They can be installed using pip and/or conda.
 - ucsc-liftover
 - selenium
 - geckodriver
+- intervaltree
 
 ### Databases
 

diff --git a/dbbuild/build-summary.txt b/dbbuild/build-summary.txt
diff --git a/dbbuild/build.py b/dbbuild/build.py
@@ -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)