Package net.maizegenetics.pangenome.processAssemblyGenomes

Class Summary
Class	Description
AssemblyProcessingUtils	This class contains methods useful for processing assembly haplotypes.
MummerScriptProcessing	This class contains methods that run mummer4 scripts, e.g.
ResizeRefBlockPlugin
PairedSimilarFragment	Class that holds reference and assembly alignment data to be sorted and filtered in a longest path algorithm.
AssemblyHaplotypesPlugin	This Class is DEPRECATED!!
FindRampSeqContigsInAssemblies	This method takes a fasta of ramp seq short sequences, and looks for them in an assembly genome.
RampSeqContigToGenomeIntervalPlugin	NOTE: this method created to aid Dan Ilut.
MummerAnalysisMetricsPlugin	This method provides summary statistics on mummer output.
SyntenicAnchors	Class originally written by Baoxing Song for post-processing minimap2 alignments.
CreateContigFastaFromAssemblyGenomePlugin	The sequence for each chromosome in the genome fasta file will be split based on N's.
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.
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.