ADAM_2.12: Core 0.36.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package ds
  Definition Classes
    adam
-  package fragment
  Definition Classes
    ds
- DatasetBoundFragmentDataset
- FragmentDataset
- InterleavedFASTQInFormatter
- ParquetUnboundFragmentDataset
- RDDBoundFragmentDataset
- Tab5InFormatter
- Tab6InFormatter

c

org.bdgenomics.adam.ds.fragment

# Tab5InFormatter 

###
Companion object Tab5InFormatter

#### class Tab5InFormatter extends InFormatter[Fragment, Fragment, FragmentDataset, Tab5InFormatter] with Logging

Linear Supertypes
Logging, InFormatter[Fragment, Fragment, FragmentDataset, Tab5InFormatter], Serializable, Serializable, AnyRef, Any
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Inherited

1. Tab5InFormatter
2. Logging
3. InFormatter
4. Serializable
5. Serializable
6. AnyRef
7. Any

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Visibility

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### Value Members

1.  final def !=(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
2.  final def ##(): Int
   Definition Classes
     AnyRef → Any
3.  final def ==(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
4.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
5.  def clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
6.  val companion: Tab5InFormatter.type
   Attributes
     protected
   Definition Classes
     Tab5InFormatter → InFormatter
7.  def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
   Attributes
     protected
   Definition Classes
     Logging
8.  def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
   Attributes
     protected
   Definition Classes
     Logging
9.  def debug(msg: ⇒ Any): Unit
   Attributes
     protected
   Definition Classes
     Logging
10.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
11.  def equals(arg0: Any): Boolean
    Definition Classes
      AnyRef → Any
12.  def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
13.  def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
14.  def error(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
15.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
16.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
17.  def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
18.  def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
19.  def info(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
20.  def isDebugEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
21.  def isErrorEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
22.  def isInfoEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
23.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
24.  def isTraceEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
25.  def isWarnEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
26.  def logger: Logger
    Attributes
      protected
    Definition Classes
      Logging
27.  def loggerName: String
    Attributes
      protected
    Definition Classes
      Logging
28.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
29.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
30.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
31.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
32.  def toString(): String
    Definition Classes
      AnyRef → Any
33.  def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
34.  def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
35.  def trace(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
36.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
37.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
38.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
39.  def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
40.  def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
41.  def warn(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
42.  def write(os: OutputStream, iter: Iterator[Fragment]): Unit

    Writes alignments to an output stream in Bowtie tab5 format.

    Writes alignments to an output stream in Bowtie tab5 format.

    In Bowtie tab5 format, each alignment or pair is on a single line. An unpaired alignment line is [name]\t[seq]\t[qual]\n. A paired-end read line is [name]\t[seq1]\t[qual1]\t[seq2]\t[qual2]\n.

    The read name for a paired-end read line is the name of the first read with the suffix trimmed.

    os

      An OutputStream connected to a process we are piping to.

    iter

      An iterator of records to write.

    Definition Classes
      Tab5InFormatter → InFormatter

### Deprecated Value Members

1.  def finalize(): Unit
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
   Deprecated

     (Since version ) see corresponding Javadoc for more information.

### Inherited from Logging

### Inherited from InFormatter[Fragment, Fragment, FragmentDataset, Tab5InFormatter]

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped