#!/usr/bin/env python

import argparse
import logging
import os
from run_breakseq2 import breakseq_top

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="BreakSeq2: A fast and accurate SV-caller using junction-mapping",
                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)

    breakseq_top.add_options(parser)

    args = parser.parse_args()

    FORMAT = '%(levelname)s %(asctime)-15s %(name)-20s %(message)s'
    logging.basicConfig(level=logging.INFO, format=FORMAT)

    breakseq_top.breakseq2_workflow(args.sample, os.path.realpath(args.bplib), os.path.realpath(args.bwa),
                                    os.path.realpath(args.samtools), args.bams, os.path.realpath(args.work),
                                    args.chromosomes,
                                    args.nthreads, args.min_span, args.min_overlap, os.path.realpath(args.reference),
                                    args.keep_temp, args.window)
#!/usr/bin/env python

import argparse
import logging
import os
from breakseq2 import breakseq_top

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="BreakSeq2: A fast and accurate SV-caller using junction-mapping",
                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)

    breakseq_top.add_options(parser)

    args = parser.parse_args()

    FORMAT = '%(levelname)s %(asctime)-15s %(name)-20s %(message)s'
    logging.basicConfig(level=logging.INFO, format=FORMAT)

    breakseq_top.breakseq2_workflow(args.sample, os.path.realpath(args.bplib), os.path.realpath(args.bwa),
                                    os.path.realpath(args.samtools), args.bams, os.path.realpath(args.work),
                                    args.chromosomes,
                                    args.nthreads, args.min_span, args.min_overlap, os.path.realpath(args.reference),
                                    args.keep_temp, args.window)
Fix circular import