def buildBAM(infile, outfile):
'''map reads with bowtie'''
track = P.snip(os.path.basename(outfile), ".bam")
job_threads = PARAMS["bowtie_threads"]
m = PipelineMapping.Bowtie()
reffile = PARAMS["samtools_genome"]
statement = m.build((infile,), outfile)
P.run()
def alignReadsToTranscriptome(infile, outfile):
'''map reads to transcriptome with bowtie'''
track = P.snip(os.path.basename(outfile), ".bam")
job_threads = PARAMS["bowtie_threads"]
m = PipelineMapping.Bowtie()
reffile = PARAMS["bowtie_transcriptome"]
bowtie_options = PARAMS["bowtie_options"]
statement = m.build((infile, ), outfile)
P.run()
def buildBAM(infile, outfile, options):
'''map reads with bowtie'''
job_threads = PARAMS["bowtie_threads"]
m = PipelineMapping.Bowtie()
reffile = PARAMS["samtools_genome"]
bowtie_options = options
statement = m.build((infile, ), outfile)
# print(statement)
P.run()