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How to read a SAM record into the SAMRecord class
I am trying to read in Array[htsjdk.samtools.SAMRecord] into the SAMRecord class and trying to get their starting position by the getAlignmentStart method of the class. I have created the SAMRecord object like this (in Scala):
// samRecordInput is an array of type Array[htsjdk.samtools.SAMRecord]
val header = new SAMFileHeader()
val samRecord = new SAMRecord(header)
How can I pass this array to the samRecord object?