# Path: nanopore/mappers/bwa.py
# class Bwa(AbstractMapper):
#     def run(self, args=""):
#         localReferenceFastaFile = os.path.join(self.getLocalTempDir(), "ref.fa") #Because BWA builds these crufty index files, copy to a temporary directory
#         system("cp %s %s" % (self.referenceFastaFile, localReferenceFastaFile))
#         system("bwa index %s" % localReferenceFastaFile)
#         system("bwa mem %s %s %s > %s" % (args, localReferenceFastaFile, self.readFastqFile, self.outputSamFile))


from nanopore.mappers.bwa import Bwa
from sonLib.bioio import system
import os

class BwaParams(Bwa):
    def run(self):
        Bwa.run(self, args="-x pacbio")

class BwaParamsChain(BwaParams):
    def run(self):
        BwaParams.run(self)
        self.chainSamFile()
        
class BwaParamsRealign(BwaParams):
    def run(self):
        BwaParams.run(self)
        self.realignSamFile()


# Path: nanopore/mappers/bwa.py
# class Bwa(AbstractMapper):
#     def run(self, args=""):
#         localReferenceFastaFile = os.path.join(self.getLocalTempDir(), "ref.fa") #Because BWA builds these crufty index files, copy to a temporary directory
#         system("cp %s %s" % (self.referenceFastaFile, localReferenceFastaFile))
#         system("bwa index %s" % localReferenceFastaFile)
#         system("bwa mem %s %s %s > %s" % (args, localReferenceFastaFile, self.readFastqFile, self.outputSamFile))


# Path: nanopore/mappers/bwa_params.py
from nanopore.mappers.bwa import Bwa
from sonLib.bioio import system
import os


class BwaParams(Bwa):
    def run(self):
        Bwa.run(self, args="-x pacbio")

class BwaParamsChain(BwaParams):
    def run(self):
        BwaParams.run(self)
        self.chainSamFile()
        
class BwaParamsRealign(BwaParams):
    def run(self):
        BwaParams.run(self)
        self.realignSamFile()


class BwaParamsRealignEm(BwaParams):