main module

mavis.validate.main.main(input, output, bam_file, stranded_bam, library, protocol, median_fragment_size, stdev_fragment_size, read_length, reference_genome, annotations, masking, blat_2bit_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()
• blat_2bit_reference (str) – path to the 2bit reference file

mavis.validate.main.samtools_v0_sort(input_bam, output_bam)

mavis.validate.main.samtools_v1_sort(input_bam, output_bam)