Pileup and coverage
Pileup and coverage
| Property Name | Default | Meaning |
|---|---|---|
| spark.biodatageeks.coverage.filterFlag | 1796 | Which SAM flags to use for filtering records. Check SAM explainer for details. |
| spark.biodatageeks.coverage.minMapQual | 0 | Minimal value of reads' mapping quality to be included in coverage/pileup calculations |
| spark.biodatageeks.pileup.useVectorizedOrcWriter | false | Whether to use vectorized ORC writer and to bypass Spark’s InternalRow serialization and write directly to the ouput file. This option is still experimental but speeds up saving results substantially. |
| spark.biodatageeks.pileup.maxBaseQuality | 40 | Specify the number of base quality values - internally used for allocating BQ counters. |
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Last modified February 1, 2023: fix:race condition for local[n] in toCoverage method (#172) (a49c32b)