def __init__(self, ctx):
super(type(self), self).__init__(ctx)
self.__get_configuration(ctx)
logging.basicConfig(level=self.log_level)
self.event_monitor = HadoopEventMonitor(self.COUNTER_CLASS,
logging.getLogger("mapper"),
ctx)
self.aligner = BwaAligner()
self.aligner.event_monitor = self.event_monitor
self.aligner.qformat = self.format
self.aligner.max_isize = self.max_isize
self.aligner.nthreads = self.nthreads
self.aligner.trim_qual = self.trim_qual
self.aligner.mmap_enabled = True
######## assemble hit processor chain
chain = FilterLink(self.event_monitor)
chain.remove_unmapped = self.remove_unmapped
chain.min_hit_quality = self.min_hit_quality
if self.__map_only:
chain.set_next(EmitSamLink(ctx, self.event_monitor))
else:
chain.set_next(MarkDuplicatesEmitter(ctx, self.event_monitor))
self.aligner.hit_visitor = chain
######## set the path to the reference index
self.ref_archive = utils.get_ref_archive(ctx.getJobConf())
self.aligner.reference = self.get_reference_root(self.ref_archive)
# part of the code is a workaround for accumulating records, see #331
isplit = InputSplit(ctx.getInputSplit())
self.split_end = isplit.offset + isplit.length
def __init__(self, ctx):
super(reducer, self).__init__(ctx)
jc = ctx.getJobConf()
logger = logging.getLogger("seqal")
jobconf = deprecation_utils.convert_job_conf(jc, self.DeprecationMap, logger)
jc_configure(self, jobconf, 'seal.seqal.log.level', 'log_level', 'INFO')
jc_configure_bool(self, jobconf, 'seal.seqal.discard_duplicates', 'discard_duplicates', False)
logging.basicConfig(level=self.log_level)
self.event_monitor = HadoopEventMonitor(self.COUNTER_CLASS, logging.getLogger("reducer"), ctx)
self.__output_sink = EmitSamLink(ctx, self.event_monitor)
def setUp(self):
self.map_ctx = map_context(None, None)
self.count_group = "Test"
self.logger = SavingLogger()
self.monitor = HadoopEventMonitor(self.count_group, self.logger, self.map_ctx)
self.emitter = EmitSamLink(self.map_ctx, self.monitor)
# create two mappings, m1, m2. We put them in self.pair
# m1 has:
# name = first
# tid = tid1
# m2 has:
# name = second
# tid = tid2
self.pair = [ SimpleMapping(), SimpleMapping() ]
self.m1, self.m2 = self.pair
self.m1.set_name("first")
self.m1.tid = "tid1"
self.m2.set_name("second")
self.m2.tid = "tid2"
def test_constructor_link(self): h = EmitSamLink(self.map_ctx, self.monitor) self.assertTrue(h.next_link is None) other = HitProcessorChainLink() h = EmitSamLink(self.map_ctx, self.monitor, other) self.assertEqual(other, h.next_link)
