bam

implicit class BiopetSamDict extends AnyRef

This class will add functionality to SAMSequenceDictionary

object InsertsizeEstimate
def sampleBamInsertSize(bamFile: File, samplingSize: Int = 10000, binSize: Int = 1000000): Int

Estimate the insertsize for one single bamfile and return the insertsize
Estimate the insertsize for one single bamfile and return the insertsize
bamFile
bamfile to estimate average insertsize from
def sampleBamMap(bamFiles: List[File]): Map[String, File]

This method will convert a list of bam files to a Map[<sampleName>, <bamFile>]
This method will convert a list of bam files to a Map[<sampleName>, <bamFile>]
Each sample may only be once in the list
bamFiles
input bam files
returns
Map of sample bam files

Exceptions thrown
def sampleBamReaderMap(bamFiles: List[File]): Map[String, (SamReader, File)]
def sampleBamsInsertSize(bamFiles: List[File], samplingSize: Int = 10000, binSize: Int = 1000000): ParMap[File, Int]

Estimate the insertsize for each bam file and return Map[<sampleBamFile>, <insertSize>]
Estimate the insertsize for each bam file and return Map[<sampleBamFile>, <insertSize>]
bamFiles
input bam files
def sampleReadGroups(readers: Map[String, (SamReader, File)]): Map[String, List[SAMReadGroupRecord]]
def sampleReadGroups(bamFiles: List[File]): Map[String, List[SAMReadGroupRecord]]

This method will return all readgroups for each sample
This method will return all readgroups for each sample
bamFiles
input bam files
returns
Map of sample readgroups

Exceptions thrown