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src/s/e/seal-0.4.0-rc2/seal/lib/mr/emit_sam_link.py   seal(Download)
 
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.io.sam_formatter import SamFormatter
 
class EmitSamLink(HitProcessorChainLink):
    def __init__(self, context, event_monitor, next_link = None):
        super(EmitSamLink, self).__init__(next_link)
        self.ctx = context
        self.output_formatter = SamFormatter(strip_pe_tag=True)

src/s/e/seal-0.4.0-rc2/tests/seal/lib/io/test_sam_formatter.py   seal(Download)
import array
 
from seal.lib.io.sam_formatter import SamFormatter
from seal.lib.aligner.mapping import SimpleMapping
 
class TestSamFormatter(unittest.TestCase):
 
    def setUp(self):
        self.mapping = SimpleMapping()
        self.f = SamFormatter()

src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/test_bwa_aligner.py   seal(Download)
import unittest
 
from seal.lib.io.sam_formatter import SamFormatter
from seal.lib.aligner.bwa.bwa_aligner import BwaAligner
 
class MappingsCollector(object):
  def __init__(self):
    self.mappings = []
    self.formatter = SamFormatter()

src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/bwa/test_bwa_aligner.py   seal(Download)
 
from seal.lib.aligner.bwa.bwa_aligner import BwaAligner
from seal.lib.io.sam_formatter import SamFormatter
import seal.lib.aligner.bwa.bwa_core as bwa
import testing_utilities as utils
    def __init__(self):
      self.sam = SamFormatter()
      self.output = StringIO.StringIO()
 
    def process(self, pair):

src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/bwa/testing_utilities.py   seal(Download)
#import seal.lib.generator as sg
import seal.lib.aligner.bwa.constants as bwa_const
from seal.lib.io.sam_formatter import SamFormatter
##---------------------------------##
# find or build the bwa executable
def read_sam_file(fname):
  formatter = SamFormatter()
  fp = open(fname)
  res = []
  for l in fp: