org.hammerlab.guacamole.readsets.io

InputFilters

case class InputFilters(overlapsLociOpt: Option[ParsedLoci], nonDuplicate: Boolean, passedVendorQualityChecks: Boolean, isPaired: Boolean, minAlignmentQuality: Int) extends Product with Serializable

Filtering reads while they are loaded can be an important optimization.

These fields are commonly used filters. For boolean fields, setting a field to true will result in filtering on that field. The result is the intersection of the filters (i.e. reads must satisfy ALL filters).

overlapsLociOpt

if set, include only mapped reads that overlap the given loci

nonDuplicate

include only reads that do not have the duplicate bit set

passedVendorQualityChecks

include only reads that do not have the failedVendorQualityChecks bit set

isPaired

include only reads are paired-end reads

minAlignmentQuality

Minimum Phred-scaled alignment score for a read

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Instance Constructors

  1. new InputFilters(overlapsLociOpt: Option[ParsedLoci], nonDuplicate: Boolean, passedVendorQualityChecks: Boolean, isPaired: Boolean, minAlignmentQuality: Int)

    overlapsLociOpt

    if set, include only mapped reads that overlap the given loci

    nonDuplicate

    include only reads that do not have the duplicate bit set

    passedVendorQualityChecks

    include only reads that do not have the failedVendorQualityChecks bit set

    isPaired

    include only reads are paired-end reads

    minAlignmentQuality

    Minimum Phred-scaled alignment score for a read

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  1. final def !=(arg0: AnyRef): Boolean

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  10. final def getClass(): Class[_]

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  11. final def isInstanceOf[T0]: Boolean

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  12. val isPaired: Boolean

    include only reads are paired-end reads

  13. def loci: ParsedLoci

  14. val minAlignmentQuality: Int

    Minimum Phred-scaled alignment score for a read

  15. final def ne(arg0: AnyRef): Boolean

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  16. val nonDuplicate: Boolean

    include only reads that do not have the duplicate bit set

  17. final def notify(): Unit

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  18. final def notifyAll(): Unit

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  19. val overlapsLociOpt: Option[ParsedLoci]

    if set, include only mapped reads that overlap the given loci

  20. val passedVendorQualityChecks: Boolean

    include only reads that do not have the failedVendorQualityChecks bit set

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  22. final def wait(): Unit

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