def realigner_config(flags_obj):
"""Creates a RealignerOptions proto based on input and default settings.
Args:
flags_obj: configuration FLAGS.
Returns:
realigner_pb2.RealignerOptions protobuf.
Raises:
ValueError: If we observe invalid flag values.
"""
ws_config = window_selector_config(flags_obj)
dbg_config = realigner_pb2.DeBruijnGraphOptions(
min_k=flags_obj.dbg_min_k,
max_k=flags_obj.dbg_max_k,
step_k=flags_obj.dbg_step_k,
min_mapq=flags_obj.dbg_min_mapq,
min_base_quality=flags_obj.dbg_min_base_quality,
min_edge_weight=flags_obj.dbg_min_edge_weight,
max_num_paths=flags_obj.dbg_max_num_paths)
aln_config = realigner_pb2.AlignerOptions(
match=flags_obj.aln_match,
mismatch=flags_obj.aln_mismatch,
gap_open=flags_obj.aln_gap_open,
gap_extend=flags_obj.aln_gap_extend,
k=flags_obj.aln_k,
error_rate=flags_obj.aln_error_rate,
max_num_of_mismatches=flags_obj.max_num_mismatches,
realignment_similarity_threshold=flags_obj.
realignment_similarity_threshold,
kmer_size=flags_obj.kmer_size,
force_alignment=False)
diagnostics = realigner_pb2.Diagnostics(
enabled=bool(flags_obj.realigner_diagnostics),
output_root=flags_obj.realigner_diagnostics,
emit_realigned_reads=flags_obj.emit_realigned_reads)
# The normalize_reads flag could came from the `flags_obj` arg, passed in
# from make_examples_options.py. It is already part of AlleleCounterOptions in
# MakeExamplesOptions. Here, we need to set it in RealignerOptions as well
# because an if statement in fast_pass_aligner.cc needs it to decide whether
# to run a specific logic.
# This is not ideal. If there's a way to improve this, please do.
normalize_reads = False
if 'normalize_reads' in flags_obj:
normalize_reads = flags_obj.normalize_reads
return realigner_pb2.RealignerOptions(
ws_config=ws_config,
dbg_config=dbg_config,
aln_config=aln_config,
diagnostics=diagnostics,
split_skip_reads=flags_obj.split_skip_reads,
normalize_reads=normalize_reads)
def make_test_aligner(self, ref_seq=None, region=None):
config = realigner_pb2.AlignerOptions(match=1,
mismatch=1,
gap_open=2,
gap_extend=1,
k=3,
error_rate=.02)
ref_seq = ref_seq or 'AAAAAAA'
region = region or ranges.make_range('ref', 10, 10 + len(ref_seq))
return aligner.Aligner(config, region, ref_seq)
def realigner_config(flags_obj):
"""Creates a RealignerOptions proto based on input and default settings.
Args:
flags_obj: configuration FLAGS.
Returns:
realigner_pb2.RealignerOptions protobuf.
Raises:
ValueError: If we observe invalid flag values.
"""
ws_config = window_selector_config(flags_obj)
dbg_config = realigner_pb2.DeBruijnGraphOptions(
min_k=flags_obj.dbg_min_k,
max_k=flags_obj.dbg_max_k,
step_k=flags_obj.dbg_step_k,
min_mapq=flags_obj.dbg_min_mapq,
min_base_quality=flags_obj.dbg_min_base_quality,
min_edge_weight=flags_obj.dbg_min_edge_weight,
max_num_paths=flags_obj.dbg_max_num_paths)
aln_config = realigner_pb2.AlignerOptions(
match=flags_obj.aln_match,
mismatch=flags_obj.aln_mismatch,
gap_open=flags_obj.aln_gap_open,
gap_extend=flags_obj.aln_gap_extend,
k=flags_obj.aln_k,
error_rate=flags_obj.aln_error_rate,
max_num_of_mismatches=flags_obj.max_num_mismatches,
realignment_similarity_threshold=flags_obj.
realignment_similarity_threshold,
kmer_size=flags_obj.kmer_size)
diagnostics = realigner_pb2.Diagnostics(
enabled=bool(flags_obj.realigner_diagnostics),
output_root=flags_obj.realigner_diagnostics,
emit_realigned_reads=flags_obj.emit_realigned_reads)
return realigner_pb2.RealignerOptions(
ws_config=ws_config,
dbg_config=dbg_config,
aln_config=aln_config,
diagnostics=diagnostics)
