[HLS-627] Improve lift_over_variants performance #285
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Signed-off-by: kianfar77 <[email protected]>
Codecov Report
@@ Coverage Diff @@
## master #285 +/- ##
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Coverage 93.62% 93.63%
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Files 92 92
Lines 4364 4367 +3
Branches 386 380 -6
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+ Hits 4086 4089 +3
Misses 278 278
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kianfar77
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Sep 4, 2020
Signed-off-by: kianfar77 <[email protected]>
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Signed-off-by: kianfar77 [email protected]
What changes are proposed in this pull request?
This PR removed the usage of htsjdk.samtools.reference.ReferenceSequence.getBaseString on long sequences and replaces it with getBases followed by converting only the desired part of the byte array to string.
Before this change, on a small cluster the transformer took close to 2 hours to do liftover on 1000 genome chr22 vcf due to a lot of string allocation and GC. After this change, the liftover takes about 10min.
How is this patch tested?
(Details)