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)[source]
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)[source]
mavis.validate.main.samtools_v1_sort(input_bam, output_bam)[source]