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mavis.validate.evidence

class mavis.validate.evidence.GenomeEvidence

inherits Evidence

mavis.validate.evidence.GenomeEvidence.generate_window()

given some input breakpoint uses the current evidence setting to determine an appropriate window/range of where one should search for supporting reads

def generate_window(self, breakpoint):

Args

  • breakpoint (Breakpoint): the breakpoint we are generating the evidence window for

Returns

  • Interval: the range where reads should be read from the bam looking for evidence for this event

class mavis.validate.evidence.TranscriptomeEvidence

inherits Evidence

mavis.validate.evidence.TranscriptomeEvidence.traverse()

given some genomic position and a distance. Uses the input transcripts to compute all possible genomic end positions at that distance if intronic positions are ignored

def traverse(self, start, distance, direction, strand=STRAND.NS, chrom=None):

Args

  • start (int): the genomic start position
  • distance (int): the amount of exonic/intergenic units to traverse
  • direction (ORIENT): the direction wrt to the positive/forward reference strand to traverse
  • strand
  • chrom

mavis.validate.evidence.TranscriptomeEvidence.distance()

give the current list of transcripts, computes the putative exonic/intergenic distance given two genomic positions. Intronic positions are ignored

Intergenic calculations are only done if exonic only fails

def distance(self, start, end, strand=STRAND.NS, chrom=None):

Args

  • start
  • end
  • strand
  • chrom

mavis.validate.evidence.TranscriptomeEvidence.generate_window()

given some input breakpoint uses the current evidence setting to determine an appropriate window/range of where one should search for supporting reads

def generate_window(self, breakpoint):

Args

  • breakpoint (Breakpoint): the breakpoint we are generating the evidence window for

Returns

  • Interval: the range where reads should be read from the bam looking for evidence for this event

mavis.validate.evidence.TranscriptomeEvidence.exon_boundary_shift_cigar()

given an input read, converts deletions to N when the deletion matches the exon boundaries. Also shifts alignments to correspond to the exon boundaries where possible

def exon_boundary_shift_cigar(self, read):

Args

  • read