Speed up BCF2 and SeekableStream integration tests#1770
Open
Conversation
BCF2EncoderDecoderUnitTest (106s → <1s): Reduce the forCombinations list from 17 to 9 values (one representative per BCF2 type plus one null per non-CHAR type). This cuts the 3-way cartesian product from 17^3=4913 to 9^3=729 test sequences while still covering all type combinations and null handling. Total tests: 13848 → 1588. SeekableStreamGZIPinputStreamIntegrationTest (82s → 4s): Reduce from 1M to 100K VCF records per test file (sufficient to exercise multi-block BGZF boundaries) and from 10 to 5 first-record-length variants. Total tests: 20 → 10. Full suite: 21,909 tests pass in 2m12s (was ~5m with 34,189 tests).
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The test suite run time is dominated by a handful of classes whose combined method/test runtime are >> 1 minute each. I'm tackling the CRAM tests that offend, which is most of them, on my cram branch. But these two also stick out.
BCF2EncoderDecoderUnitTest (106s → <1s):
Reduce the forCombinations list from 17 to 9 values (one representative
per BCF2 type plus one null per non-CHAR type). This cuts the 3-way
cartesian product from 17^3=4913 to 9^3=729 test sequences while still
covering all type combinations and null handling. Total tests: 13848 → 1588.
SeekableStreamGZIPinputStreamIntegrationTest (82s → 4s):
Reduce from 1M to 100K VCF records per test file (sufficient to exercise
multi-block BGZF boundaries) and from 10 to 5 first-record-length
variants. Total tests: 20 → 10.
Full suite: 21,909 tests pass in 2m12s (was ~5m with 34,189 tests).
Things to think about before submitting: