def generatedNames(self):
try:
# open dataset on generated BAM file, read in names
dataset = PacBioBam.DataSet(self.generatedBamFn)
entireFile = PacBioBam.EntireFileQuery(dataset)
names_out = []
for record in PacBioBam.Iterate(entireFile):
names_out.append(record.FullName())
return names_out
except RuntimeError:
self.assertTrue(False) # should not throw
def originalNames(self):
# loop over original file, store names, write to generated file
try:
file = PacBioBam.BamFile(self.ex2BamFn)
writer = PacBioBam.BamWriter(self.generatedBamFn, file.Header())
dataset = PacBioBam.DataSet(self.ex2BamFn)
entireFile = PacBioBam.EntireFileQuery(dataset)
names_in = []
for record in PacBioBam.Iterate(entireFile):
names_in.append(record.FullName())
writer.Write(record)
return names_in
except RuntimeError:
self.assertTrue(False) # should not throw