ADAM_2.12: Core 1.0 API < Back
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# Packages

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-  package org
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-  package bdgenomics
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-  package adam
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    bdgenomics
-  package converters
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    adam
- AlignmentConverter
- DefaultHeaderLines
- VariantContextConverter

o

org.bdgenomics.adam.converters

# AlignmentConverter 

###
Companion class AlignmentConverter

#### object AlignmentConverter extends Serializable

Singleton object to assist with converting Alignments.

Singleton object exists due to cross reference from org.bdgenomics.adam.rdd.read.AlignmentDatasetFunctions.

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Serializable, Serializable, AnyRef, Any
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15.  def processingSteps(header: SAMFileHeader): Seq[ProcessingStep]

    Return the processing steps in the specified SAM file header.

    Return the processing steps in the specified SAM file header.

    header

      SAM file header

    returns

      the processing steps in the specified SAM file header

16.  def readGroups(header: SAMFileHeader): ReadGroupDictionary

    Return the read groups in the specified SAM file header.

    Return the read groups in the specified SAM file header.

    header

      SAM file header

    returns

      the read groups in the specified SAM file header

17.  def readNameHasPairedSuffix(adamRecord: Alignment): Boolean

    Checks to see if a read name has a index suffix.

    Checks to see if a read name has a index suffix.

    Read names frequently end in a "/%d" suffix, where the digit at the end signifies the number of this read in the sequenced fragment. E.g., for an Illumina paired-end protocol, the first read in the pair will have a "/1" suffix, while the second read in the pair will have a "/2" suffix.

    adamRecord

      Record to check.

    returns

      True if the read ends in a read number suffix.

18.  def references(header: SAMFileHeader): SequenceDictionary

    Return the references in the specified SAM file header.

    Return the references in the specified SAM file header.

    header

      SAM file header

    returns

      the references in the specified SAM file header

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