Alignment

Value Members

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

   

   Definition Classes

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2. final def ##(): Int

   

   Definition Classes

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3. final def ==(arg0: Any): Boolean

   

   Definition Classes

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4. final def asInstanceOf[T0]: T0

   

   Definition Classes

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5. val cigar: String

   

   CIGAR string

6. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

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   Annotations

   @throws( ... )

7. val contig: String

   

   Reference sequence NAME

8. final def eq(arg0: AnyRef): Boolean

   

   Definition Classes

   AnyRef

9. def finalize(): Unit

   

   Attributes

   protected[java.lang]

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   @throws( classOf[java.lang.Throwable] )

10. val flag: Int

    

    bitwise FLAG

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

    

    Definition Classes

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12. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

13. val mapq: Int

    

    MAPping Quality

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

    

    Definition Classes

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15. final def notify(): Unit

    

    Definition Classes

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16. final def notifyAll(): Unit

    

    Definition Classes

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17. val pnext: Int

    

    Position of the mate/next read

18. val pos: Int

    

    1-based leftmost mapping POSition

19. val pos_end: Int

    

    1-based rightmost mapping POSition of a read

20. val pos_start: Int

    

    1-based leftmost mapping POSition of a read

21. val qname: String

    

    Query template NAME

22. val qual: String

    

    ASCII of Phred-scaled base QUALity+33

23. val rnext: String

    

    Reference name of the mate/next read

24. val sample_id: String

    

    SAMPLE name

25. val seq: String

    

    segment SEQuence

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

    

    Definition Classes

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27. val tag_AM: Option[Int]

    

    The smallest template-independent mapping quality in the template

28. val tag_AS: Option[Int]

    

    Alignment score generated by aligner

29. val tag_BC: Option[String]

    

    Barcode sequence identifying the sample

30. val tag_BQ: Option[String]

    

    Offset to base alignment quality (BAQ)

31. val tag_BZ: Option[String]

    

    Phred quality of the unique molecular barcode bases in the OX tag

32. val tag_CB: Option[String]

    

    Cell identifier

33. val tag_CC: Option[String]

    

    Reference name of the next hit

34. val tag_CG: Option[String]

    

    BAM only: CIGAR in BAM's binary encoding if (and only if) it consists of $>$65535 operators

35. val tag_CM: Option[Int]

    

    Edit distance between the color sequence and the color reference (see also NM)

36. val tag_CO: Option[String]

    

    Free-text comments

37. val tag_CP: Option[Int]

    

    Leftmost coordinate of the next hit

38. val tag_CQ: Option[String]

    

    Color read base qualities

39. val tag_CR: Option[String]

    

    Cellular barcode sequence bases (uncorrected)

40. val tag_CS: Option[String]

    

    Color read sequence

41. val tag_CT: Option[String]

    

    Complete read annotation tag, used for consensus annotation dummy features

42. val tag_CY: Option[String]

    

    Phred quality of the cellular barcode sequence in the CR tag

43. val tag_E2: Option[String]

    

    The 2nd most likely base calls

44. val tag_FI: Option[Int]

    

    The index of segment in the template

45. val tag_FS: Option[String]

    

    Segment suffix

46. val tag_FZ: Option[String]

    

    Flow signal intensities

47. val tag_H0: Option[Int]

    

    Number of perfect hits

48. val tag_H1: Option[Int]

    

    Number of 1-difference hits (see also NM)

49. val tag_H2: Option[Int]

    

    Number of 2-difference hits

50. val tag_HI: Option[Int]

    

    Query hit index

51. val tag_IH: Option[Int]

    

    Query hit total count

52. val tag_LB: Option[String]

    

    Library

53. val tag_MC: Option[String]

    

    CIGAR string for mate/next segment

54. val tag_MD: Option[String]

    

    String for mismatching positions

55. val tag_MI: Option[String]

    

    Molecular identifier

56. val tag_MQ: Option[Int]

    

    Mapping quality of the mate/next segment

57. val tag_NH: Option[Int]

    

    Number of reported alignments that contain the query in the current record

58. val tag_NM: Option[Int]

    

    Edit distance to the reference

59. val tag_OA: Option[String]

    

    Original alignment

60. val tag_OC: Option[String]

    

    Original CIGAR (deprecated

61. val tag_OP: Option[Int]

    

    Original mapping position (deprecated

62. val tag_OQ: Option[String]

    

    Original base quality

63. val tag_OX: Option[String]

    

    Original unique molecular barcode bases

64. val tag_PG: Option[String]

    

    Program

65. val tag_PQ: Option[Int]

    

    Phred likelihood of the template

66. val tag_PT: Option[String]

    

    Read annotations for parts of the padded read sequence

67. val tag_PU: Option[String]

    

    Platform unit

68. val tag_Q2: Option[String]

    

    Phred quality of the mate/next segment sequence in the R2 tag

69. val tag_QT: Option[String]

    

    Phred quality of the sample barcode sequence in the BC tag

70. val tag_QX: Option[String]

    

    Quality score of the unique molecular identifier in the RX tag

71. val tag_R2: Option[String]

    

    Sequence of the mate/next segment in the template

72. val tag_RG: Option[String]

    

    Read group

73. val tag_RX: Option[String]

    

    Sequence bases of the (possibly corrected) unique molecular identifier

74. val tag_SA: Option[String]

    

    Other canonical alignments in a chimeric alignment

75. val tag_SM: Option[Int]

    

    Template-independent mapping quality

76. val tag_TC: Option[Int]

    

    The number of segments in the template

77. val tag_U2: Option[String]

    

    Phred probability of the 2nd call being wrong conditional on the best being wrong

78. val tag_UQ: Option[Int]

    

    Phred likelihood of the segment, conditional on the mapping being correct

79. val tlen: Int

    

    observed Template LENgth

80. final def wait(): Unit

    

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    @throws( ... )

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

    

    Definition Classes

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    @throws( ... )

82. final def wait(arg0: Long): Unit

    

    Definition Classes

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    @throws( ... )