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<a href="https://github.com/bigdatagenomics/adam/commit/<a class=hub.com/bigdatagenomics/adam/commit/b1fce67705ab49815a9707938972a7d1c0a5f2f4">b1fce6770<a href="https://github.com/bigdatagenomics/adam/commit/b1fce67705ab49815a9707938972a7d1c0a5f2f4">">[ADAM-1358] Refactor BQSR to improve performance and legibility. Resolves #1358. * Adds instrumentation to BQSR. * Changed SnpTable to remove RichVariant conversion, use VariantRDD API. * Refactoring SnpTable to eliminate per-residue costly masked site lookup. * Restructuring core of SnpTable around an array to improve GC performance. Additionally, wrote custom serializer to improve serialization performance. * Added test suite for SnpTable, to test table creation. * Refactored SnpTable to use an IntervalArray-like approach. This approach improves masked site lookup performance by 50%. * Added tests to SnpTableSuite to cover lookup case, and reenabled tests in BaseQualityRecalibrationSuite. * Adding unit test coverage to covariates * Revert &quot;[ADAM-775] Allow all IUPAC codes in BQSR" This reverts commit </a><a class="double-link" href="https://github.com/bigdatagenomics/adam/commit/<a class="double-link" href="https://github.com/bigdatagenomics/adam/commit/207eebaf3dbf6f01e5b8398b2af388ee70c862aa">207eebaf3</a>">207eebaf3</a><a href="https://github.com/bigdatagenomics/adam/commit/b1fce67705ab49815a9707938972a7d1c0a5f2f4">. * Pulled Seq allocation for base check out into an immutable set. * Rewrote dinuc covariate. 50% improvement in performance. * Rewrite main BQSR aggregate as reduce by key * Added tests to recalibrator, recalibration table. * Majorly refactors of BQSR tables. * Starting to factor out the QualityScore class * Refactoring CovariateKey to reduce size in memory * Eliminated `org.bdgenomics.adam.rich.DecadentRead` (partially resolves #577) * Refactor CovariateKey to store record group ID instead of record group name. * Removed `org.bdgenomics.adam.models.QualityScore`. * Split multi-class files into one class per file (excepting private classes) to improve navigability. * Scaladoc all the recalibrators! You get a scaladoc! And you get a scaladoc!
4694 of 5826 relevant lines covered (80.57%)
0.81 hits per line
Coverage | ∆ | File | Lines | Relevant | Covered | Missed | Hits/Line |
---|---|---|---|---|---|---|---|
0.0 | ...rg/bdgenomics/adam/rdd/read/SingleReadBucket.scala | 183 + 45 | 4 - 62 | 0 - 45 | 4 - 17 | 0.0 - 5 | |
0.0 | ...scala/org/bdgenomics/adam/rdd/read/MDTagging.scala | 107 + 96 | 1 - 5 | 0 - 5 | 1 | 0.0 - 1.0 | |
0.0 | .../org/bdgenomics/adam/rdd/variant/GenotypeRDD.scala | 179 | 1 | 0 | 1 | 0.0 | |
0.0 | .../bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala | 958 + 934 | 1 - 11 | 0 - 8 | 1 - 3 | 0.0 - 1.0 | |
0.0 | ...scala/org/bdgenomics/adam/util/ParquetLogger.scala | 35 | 2 | 0 | 2 | 0.0 | |
0.0 | .../bdgenomics/adam/util/ParquetFileTraversable.scala | 86 | 23 | 0 | 23 | 0.0 | |
0.0 | ...in/scala/org/bdgenomics/adam/util/TwoBitFile.scala | 234 | 6 | 0 | 6 | 0.0 | |
0.0 | ...dgenomics/adam/rdd/variant/VariantContextRDD.scala | 234 | 1 | 0 | 1 | 0.0 | |
0.0 | ...a/org/bdgenomics/adam/rdd/variant/VariantRDD.scala | 151 | 1 | 0 | 1 | 0.0 | |
0.0 | ...org/bdgenomics/adam/rdd/fragment/FragmentRDD.scala | 157 + 84 | 1 - 45 | 0 - 6 | 1 - 39 | 0.0 - 12 |