class ReadRealigner(object):
"""An abstraction layer for different short read realigners."""
def __init__(self, lack_bin, show_progress):
self.lack = Lack(lack_bin, show_progress=show_progress)
def run_alignment(self, query_fasta_path, query_sam_path, ref_seq_paths,
output_sam_path, nomatch_path, threads, accuracy):
self.lack.realign_reads(query_fasta_path,
query_sam_path,
ref_seq_paths,
output_sam_path,
nonmatch_path=nomatch_path, threads=threads,
accuracy=accuracy)
def __init__(self, lack_bin, show_progress):
self.lack = Lack(lack_bin, show_progress=show_progress)
