main module

mavis.validate.main.main(inputs, output, bam_file, strand_specific, library, protocol, median_fragment_size, stdev_fragment_size, read_length, reference_genome, annotations, masking, aligner_reference, start_time=1558720095, **kwargs)

Parameters:

• inputs (list) – list of input files containing the breakpoint pairs
• output (str) – path to the output directory
• bam_file (str) – path the bam file
• strand_specific (bool) – flag to indicate the input bam is using a strand specific protocol
• median_fragment_size (int) – the median fragment size
• stdev_fragment_size (int) – the standard deviation in fragment size
• read_length (int) – read length
• reference_genome (ReferenceFile) – see load_reference_genome()
• annotations (ReferenceFile) – see load_reference_genes()
• masking (ReferenceFile) – see load_masking_regions()
• aligner_reference (ReferenceFile) – path to the aligner reference file (e.g 2bit file for blat)