Package net.maizegenetics.pangenome.processAssemblyGenomes

Class Summary

Class	Description
AssemblyHaplotypesPlugin	Process Assemblies - both anchor and interanchor.
AssemblyProcessingUtils	This class contains methods useful for processing assembly haplotypes.
CreateContigFastaFromAssemblyGenomePlugin	The sequence for each chromosome in the genome fasta file will be split based on N's.
FindRampSeqContigsInAssemblies	This method takes a fasta of ramp seq short sequences, and looks for them in an assembly genome.
Mummer4DoonerBZStats	This method takes a coords file, the genome fastas, ranges to be covered Prints out tab-delimited file of metrics related to the region.
MummerAnalysisMetricsPlugin	This method provides summary statistics on mummer output.
MummerScriptProcessing	This class contains methods that run mummer4 scripts, e.g.
RampSeqContigToGenomeIntervalPlugin	NOTE: this method created to aid Dan Ilut.
RedirectStreams	This comes from https://stackoverflow.com/questions/35706921/redirecting-the-output-of-a-process-into-the-input-of-another-process-using-proc/35709166 It is used to aid in piping output from 1 ProcessBuilder command to another.
ResizeRefBlockPlugin