main module

mavis.cluster.main.main(inputs, output, stranded_bam, library, protocol, masking, cluster_clique_size, cluster_radius, uninformative_filter, max_proximity, annotations, min_clusters_per_file, max_files, **kwargs)

Parameters:

• inputs (List of str) – list of input files to read
• output (str) – path to the output directory
• stranded_bam (bool) – is the bam using a strand specific protocol
• library (str) – the library to look for in each of the input files
• protocol (PROTOCOL) – the sequence protocol (genome or transcriptome)
• masking (object) – see load_masking_regions()
• cluster_clique_size (int) – the maximum size of cliques to search for using the exact algorithm
• cluster_radius (int) – distance (in breakpoint pairs) used in deciding to join bpps in a cluster
• uninformative_filter (bool) – if True then clusters should be filtered out if they are not within a specified (max_proximity) distance to any annotation
• max_proximity (int) – the maximum distance away an annotation can be before the uninformative_filter is applied
• annotations (object) – see load_reference_genes()
• min_clusters_per_file (int) – the minimum number of clusters to output to a file
• max_files (int) – the maximum number of files to split clusters into