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1.  final def !=(arg0: Any): Boolean

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2.  final def ##(): Int

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3.  final def ==(arg0: Any): Boolean

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4.  final def asInstanceOf[T0]: T0

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5.  def clone(): AnyRef

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6.  def compatibleFragments(feat: Feature, firstOfPairStrandOnTranscript: Orientation): Iterator[(SAMRecord, SAMRecord)]

   Returns an iterator over pairs of SAMRecords that are compatible with the Feature.

   Returns an iterator over pairs of SAMRecords that are compatible with the Feature.

   Each returned pair is a mate pair and is in the order (first of pair, second of pair).

   Returned records are fully contained in the Feature, originate from fragments transcribed from the same strand if strand specific, and have compatible introns as defined in feature.Region.containsCompatibleIntrons.

   Only mate pairs with both mates compatible with the Feature and evaluating to true under isValid are returned. Only primary alignments are used.

   The returned iterator is in no particular order.

   Throws IllegalArgumentException if records are not paired.

   feat

   The Feature

   firstOfPairStrandOnTranscript

   Strand relative to transcription strand of read 1 (if reads are paired) or all reads (if unpaired). If read 1 maps to the transcription strand, this parameter should be Plus. If read 1 maps to the opposite of the transcription strand, this parameter should be Minus. If reads are not strand-specific, this parameter should be Unstranded.

7.  def compatibleRecords(feat: Feature, firstOfPairStrandOnTranscript: Orientation): Iterator[SAMRecord]

   Returns an iterator over SAMRecords that are compatible with the Feature.

   Returns an iterator over SAMRecords that are compatible with the Feature.

   In other words, records are fully contained in the Feature, originate from fragments transcribed from the same strand if strand specific, and have compatible introns as defined in feature.Region.containsCompatibleIntrons.

   Only returns records evaluating to true under isValid.

   feat

   The Feature

   firstOfPairStrandOnTranscript

   Strand relative to transcription strand of read 1 (if reads are paired) or all reads (if unpaired). If read 1 maps to the transcription strand, this parameter should be Plus. If read 1 maps to the opposite of the transcription strand, this parameter should be Minus. If reads are not strand-specific, this parameter should be Unstranded.

   returns

   Iterator over SAMRecords that are compatible with the Feature

8.  def countCompatibleFragments(feat: Feature, firstOfPairStrandOnTranscript: Orientation): Int

   Returns the number of fragments that are compatible with the Feature.

   Returns the number of fragments that are compatible with the Feature.

   Fragments are pairs of SAMRecords if reads are paired, or single SAMRecords if reads are unpaired.

   Included records are fully contained in the Feature, originate from fragments transcribed from the same strand if strand specific, and have compatible introns as defined in feature.Region.containsCompatibleIntrons.

   If reads are paired, only mate pairs with both mates compatible with the Feature and evaluating to true under isValid are included. Only primary alignments are used.

   feat

   The Feature

   firstOfPairStrandOnTranscript

   Strand relative to transcription strand of read 1 (if reads are paired) or all reads (if unpaired). If read 1 maps to the transcription strand, this parameter should be Plus. If read 1 maps to the opposite of the transcription strand, this parameter should be Minus. If reads are not strand-specific, this parameter should be Unstranded.

   returns

   The number of compatible fragments defined as complete pairs if paired, or single records if unpaired.

9.  def countCompatibleRecords(feat: Feature, firstOfPairStrandOnTranscript: Orientation): Int

   Returns the number of SAMRecords that are compatible with the Feature.

   Returns the number of SAMRecords that are compatible with the Feature.

   In other words, records are fully contained in the Feature, originate from fragments transcribed from the same strand if strand specific, and have compatible introns as defined in feature.Region.containsCompatibleIntrons.

   Only counts records evaluating to true under isValid.

   feat

   The Feature

   firstOfPairStrandOnTranscript

   Strand relative to transcription strand of read 1 (if reads are paired) or all reads (if unpaired). If read 1 maps to the transcription strand, this parameter should be Plus. If read 1 maps to the opposite of the transcription strand, this parameter should be Minus. If reads are not strand-specific, this parameter should be Unstranded.

   returns

   Number of SAMRecords that are compatible with the Feature

10.  final def eq(arg0: AnyRef): Boolean

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11.  def equals(arg0: Any): Boolean

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12.  def finalize(): Unit

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13.  final def getClass(): Class[_]

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14.  def hashCode(): Int

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15.  final def isInstanceOf[T0]: Boolean

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16.  val isValid: (SAMRecord) ⇒ Boolean
17.  def iterator: Iterator[SAMRecord]

    Returns an iterator over all records in the reader evaluating to true under isValid.

18.  def makeReader: htsjdk.samtools.SamReader

    Returns a htsjdk.samtools.SamReader reading from the same file as this object.

    Returns a htsjdk.samtools.SamReader reading from the same file as this object.

    Use this if you want the additional functionality provided by that class. But beware, htsjdk.samtools.SamReader objects are mutable. Also, these objects and iterators over them must be closed.

19.  final def ne(arg0: AnyRef): Boolean

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20.  final def notify(): Unit

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21.  final def notifyAll(): Unit

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22.  final def synchronized[T0](arg0: ⇒ T0): T0

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23.  def toString(): String

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24.  final def wait(): Unit

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25.  final def wait(arg0: Long, arg1: Int): Unit

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26.  final def wait(arg0: Long): Unit

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