getVariantContextsfromMAF

fun getVariantContextsfromMAF(mafFile: String, refSeqs: Map<String, NucSeq>, sampleName: String, fillGaps: Boolean = false, twoGvcfs: Boolean = false, outJustGT: Boolean = false, outputType: MAFToGVCF.OUTPUT_TYPE = OUTPUT_TYPE.gvcf, delAsSymbolic: Boolean = false, maxDeletionSize: Int = 0, anchorwaveLegacy: Boolean = false): Map<String, List<AssemblyVariantInfo>>

This function creates a list of MAFRecords records which will be further processed by the calling routing