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nl.biopet.utils.ngs.bam

InsertsizeEstimate

Related Doc: package bam

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object InsertsizeEstimate

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  15. def regionInsertSize(inputBam: File, bedRecord: BedRecord, samplingSize: Int = 10000): Option[Int]

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  16. def regionsInsertSize(inputBam: File, contig: String, start: Int, end: Int, samplingSize: Int = 10000, binSize: Int = 1000000): Option[Int]

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    Estimate the insertsize of fragments within the given contig.

    Estimate the insertsize of fragments within the given contig. Uses the properly paired reads according to flags set by the aligner

    inputBam

    input bam file

    contig

    contig to scan for

    end

    position to stop scanning

    returns

    Int with insertsize for this contig

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