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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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
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the processing steps in the specified SAM file header
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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
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the read groups in the specified SAM file header
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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.
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Record to check.
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True if the read ends in a read number suffix.
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references(header: SAMFileHeader): SequenceDictionary
Return the references in the specified SAM file header.
Return the references in the specified SAM file header.
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SAM file header
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the references in the specified SAM file header
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