Preprocessing : pp

Preprocessing : `pp`#

Extracting gap from path, preprocessing recipes.

`pp.read_Verkko`	Prepares the Verkko environment by creating necessary directories, locking the original directory, and loading the paths file for further processing.
`pp.readChr`	Read the chromosome assignment results and store them in the object.
`pp.readNode`
`pp.readScfmap`
`pp.writeFixedPaths`	Writes the fixed paths to a file.
`pp.save_Verkko`	Save the Verkko fillet object to a file using pickle.
`pp.load_Verkko`	Load the Verkko fillet object from a file using pickle.
`pp.mkCNSdir`	Creates a new CNS directory by creating symbolic links to the original verkko directory.
`pp.updateCNSdir_missingEdges`	Updates the CNS directory by handling missing edges and creating necessary symbolic links or files.
`pp.loadGiraffe`	Load the object of Giraffe genome from a file using pickle.
`pp.readGaf`	Reads a GAF file and stores it as a pandas DataFrame in the provided object.
`pp.getQV`	Reads a QV (Quality Value) file, parses it, and attaches the resulting DataFrame to the provided object.

`pp.find_intra_telo`	Find the internal telomeres in the assembly.
`pp.find_reads_intra_telo`	Find the reads support for the additional artifical sequences outside of the telomere.
`pp.findGaps`	Find gaps in the 'path' column of the DataFrame and store the result in the 'gaps' column.
`pp.searchSplit`	Searches for paths containing all specified nodes with a minimum mapping quality and length.
`pp.searchNodes`	Extracts and filters paths containing specific nodes from the graph alignment file (GAF).
`pp.highlight_nodes`	Highlight the nodes in the obj.paths DataFrame.
`pp.fillGaps`	Fills gaps for a specific gapId, updates the 'fixedPath', 'startMatch', 'endMatch', and 'finalGaf' columns.
`pp.estLoops`	Estimate the number of loops between two nodes in the graph.
`pp.checkGapFilling`	This function checks and prints the number of filled gaps in the 'gap' DataFrame and shows the progress bar for gap filling.
`pp.connectContigs`	Connects two contigs by adding a gap between them.
`pp.naming_contigs`	Rename the contigs based on the provided chromosome map file.
`pp.find_multi_used_node`	Find nodes that are used in more than one path.
`pp.find_hic_support`	Find HiC support for a specific node.
`pp.deleteGap`	Deletes a gap from the 'gap' DataFrame for a specific gapId.
`pp.impute_depth`
`pp.calNodeDepth`	Plot the depth of nodes in the graph.
`pp.detectBrokenContigs`	Find contigs that assigned same chromosome and haplotype.

Get the node and chromosome mapping from the VerkkoFillet object.