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src/s/e/seal-0.4.0-rc2/seal/seqal/reducer.py   seal(Download)
 
import seal.lib.io.protobuf_mapping as protobuf_mapping
from seal.lib.mr.hadoop_event_monitor import HadoopEventMonitor
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.mr.emit_sam_link import EmitSamLink
        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)
 

src/s/e/seal-0.4.0-rc2/seal/seqal/mapper.py   seal(Download)
from seal.lib.mr.emit_sam_link import EmitSamLink
from seal.lib.mr.filter_link import FilterLink
from seal.lib.mr.hadoop_event_monitor import HadoopEventMonitor
import seal.lib.deprecation_utils as deprecation_utils
import seqal_app
    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)

src/s/e/seal-0.4.0-rc2/tests/seal/lib/mr/test_emit_sam_link.py   seal(Download)
from seal.lib.mr.emit_sam_link import EmitSamLink
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.mr.hadoop_event_monitor import HadoopEventMonitor
from seal.lib.mr.test_utils import map_context, SavingLogger
from seal.lib.aligner.mapping import *
    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)

src/s/e/seal-0.4.0-rc2/tests/seal/seqal/test_mark_duplicates_emitter.py   seal(Download)
import seal.lib.io.protobuf_mapping as proto
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.mr.hadoop_event_monitor import HadoopEventMonitor
from seal.seqal.mapper import MarkDuplicatesEmitter
from seal.seqal.seqal_app import PAIR_STRING, UNMAPPED_STRING
    def setUp(self):
        self.ctx = map_context(None, None)
        self.count_group = "Test"
        self.logger = SavingLogger()
        self.monitor = HadoopEventMonitor(self.count_group, self.logger, self.ctx)