main module

mavis.validate.main.main(input, output, bam_file, stranded_bam, library, protocol, median_fragment_size, stdev_fragment_size, read_length, reference_genome, reference_genome_filename, annotations, masking, aligner_reference, samtools_version, **kwargs)

Parameters:

• input (str) – the input file containing the breakpoint pairs
• output (str) – path to the output directory
• bam_file (str) – path the bam file
• stranded_bam (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 (Object) – see load_reference_genome()
• annotations (object) – see load_reference_genes()
• masking (object) – see load_masking_regions()
• aligner_reference (str) – path to the aligner reference file (e.g 2bit file for blat)