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src/s/e/seal-0.4.0-rc2/seal/seqal/reducer.py   seal(Download)
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
import seal.lib.deprecation_utils as deprecation_utils
import seqal_app
 
        self.event_monitor = HadoopEventMonitor(self.COUNTER_CLASS, logging.getLogger("reducer"), ctx)
        self.__output_sink = EmitSamLink(ctx, self.event_monitor)
 
    def __process_unmapped_pairs(self, ctx):

src/s/e/seal-0.4.0-rc2/seal/seqal/mapper.py   seal(Download)
import seal.lib.mr.utils as utils
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
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
        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) )

src/s/e/seal-0.4.0-rc2/tests/seal/lib/mr/test_emit_sam_link.py   seal(Download)
import re
 
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
        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:
    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)