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src/s/e/seal-0.4.0-rc2/seal/seqal/mapper.py   seal(Download)
from pydoop.utils import jc_configure, jc_configure_int, jc_configure_bool
 
from seal.lib.aligner.bwa.bwa_aligner import BwaAligner, BWA_INDEX_EXT
import seal.lib.io.protobuf_mapping as protobuf_mapping
import seal.lib.mr.utils as utils
              my_reference/irrelevant_file
        """
        index_paths = filter(lambda tpl: tpl[1].lstrip('.') in BWA_INDEX_EXT,
                                map(os.path.splitext, os.listdir(ref_dir)))
        roots = set( zip(*index_paths)[0] )
        if len(roots) == 0:
            raise(ValueError, "Missing references.  Didn't find any files with required extensions (%s) at path %s" % (BWA_INDEX_EXT, ref_dir))