def analyze_coverage(self, bam):
self.coverage.run(bam, self, method='accurate')
for split in self.splits:
split.coverage = Coverage()
split.coverage.c = self.coverage.c[split.start:split.end]
split.coverage.process_c(split.coverage.c)
def analyze_coverage(self, bam, progress):
contig_coverage = []
for split in self.splits:
progress.update('Coverage (split: %d of %d)' %
(split.order, len(self.splits)))
split.coverage = Coverage()
split.coverage.run(bam, split)
contig_coverage.extend(split.coverage.c)
self.coverage.process_c(contig_coverage)
def __init__(self, name):
self.name = name
self.parent = None
self.splits = []
self.length = 0
self.abundance = 0.0
self.coverage = Coverage()
self.min_coverage_for_variability = 10
self.report_variability_full = False
def analyze_coverage(self, bam):
contig_coverage = []
counter = 1
for split in self.splits:
split.coverage = Coverage()
split.coverage.run(bam, split)
contig_coverage.extend(split.coverage.c)
counter += 1
self.coverage.process_c(contig_coverage)
def analyze_coverage(self, bam):
contig_coverage = []
counter = 1
for split in self.splits:
split.coverage = Coverage()
split.coverage.run(bam, split,
ignore_orphans=self.ignore_orphans,
max_coverage_depth=self.max_coverage_depth)
contig_coverage.extend(split.coverage.c)
counter += 1
self.coverage.process_c(contig_coverage)
def __init__(self, name):
self.name = name
self.sequence = None
self.parent = None
self.splits = []
self.length = 0
self.abundance = 0.0
self.coverage = Coverage()
self.min_coverage_for_variability = 10
self.skip_SNV_profiling = False
self.report_variability_full = False
self.ignore_orphans = False
self.max_coverage_depth = constants.max_depth_for_coverage
self.codon_frequencies_dict = {}
def analyze_coverage(self, bam, progress):
contig_coverage = []
num_splits = len(self.splits)
counter = 1
for split in self.splits:
progress.update('Coverage (split: %d of %d)' %
(counter, num_splits))
split.coverage = Coverage()
split.coverage.run(bam, split)
contig_coverage.extend(split.coverage.c)
counter += 1
self.coverage.process_c(contig_coverage)
