PrefilterReadsArgs

abstract val autosomalOnly: Boolean

True if we want to restrict our reads to the autosomal chromosomes.

abstract val keepDuplicates: Boolean

True if we want to keep reads marked as sequencing duplicates.

abstract val keepMitochondrialChromosome: Boolean

True if we want to keep reads aligned to the mitochondrial chromosome.

abstract val keepNonPrimary: Boolean

If true, keeps secondary/supplemental alignments.

abstract val minMappingQuality: Int

The minimum mapping quality of read to keep.

final def !=(arg0: AnyRef): Boolean

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: AnyRef): Boolean

final def ==(arg0: Any): Boolean

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def equals(arg0: Any): Boolean

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final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

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