Skip to content

Commit

Permalink
fix(call): seed not being passed to caller
Browse files Browse the repository at this point in the history
  • Loading branch information
davidlougheed committed Feb 13, 2024
1 parent 339114a commit c68314d
Showing 1 changed file with 5 additions and 1 deletion.
6 changes: 5 additions & 1 deletion strkit/call/params.py
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ def __init__(
respect_ref: bool = False,
count_kmers: str = "none", # "none" | "peak" | "read"
consensus: bool = False,
# ---
log_level: int = logging.WARNING,
seed: Optional[int] = None,
processes: int = 1,
Expand All @@ -56,6 +57,7 @@ def __init__(
self.respect_ref: bool = respect_ref
self.count_kmers: str = count_kmers
self.consensus: bool = consensus
# ---
self.log_level: int = log_level
self.seed: Optional[int] = seed
self.processes: int = processes
Expand Down Expand Up @@ -98,14 +100,15 @@ def from_args(cls, logger: logging.Logger, p_args):
realign=p_args.realign,
hq=p_args.hq,
use_hp=p_args.use_hp,
# incorporate_snvs=p_args.incorporate_snvs,
snv_vcf=p_args.incorporate_snvs,
targeted=p_args.targeted,
fractional=p_args.fractional,
respect_ref=p_args.respect_ref,
count_kmers=p_args.count_kmers,
consensus=p_args.consensus or not (not p_args.vcf), # Consensus calculation is required for VCF output.
# ---
log_level=log_levels[p_args.log_level],
seed=p_args.seed,
processes=p_args.processes,
)

Expand All @@ -129,5 +132,6 @@ def to_dict(self, as_inputted: bool = False):
"count_kmers": self.count_kmers,
"consensus": self.consensus,
"log_level": self.log_level,
"Seed": self.seed,
"processes": self.processes,
}

0 comments on commit c68314d

Please sign in to comment.