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Mem dev #6

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merged 4 commits into from
Mar 25, 2024
Merged

Mem dev #6

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7ed8138
Not storign CIGARs for minimap2 AS mode
Mar 12, 2024
b188edf
Merge branch 'main' into mem-dev
bkille Mar 25, 2024
a6f3c8e
Update minimap2_AS flag to current CLI flags
bkille Mar 25, 2024
2d70adf
Update version
bkille Mar 25, 2024
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6 changes: 4 additions & 2 deletions lemur
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ import numpy as np
import pysam


__version__ = "1.0.0"
__version__ = "1.0.1"


def CTRLChandler(signum, frame):
Expand Down Expand Up @@ -422,7 +422,8 @@ class LemurRunEnv():

P_rgs_data["Read_ID"].append(qname)
P_rgs_data["Target_ID"].append(species_tid)
P_rgs_data["cigar"].append(cigar)
if not self.args.aln_score == "AS":
P_rgs_data["cigar"].append(cigar)
P_rgs_data["Gene"].append(gene)
P_rgs_data["Reference"].append(aln.reference_name)
P_rgs_data["aln_len"].append(self.__get_aln_len(aln))
Expand Down Expand Up @@ -459,6 +460,7 @@ class LemurRunEnv():
repeat(self.fixed_cigar)))

del P_rgs_data["cigar"]

self.P_rgs_df = pd.DataFrame(data=P_rgs_data)
self.P_rgs_df["max_aln_len"] = self.P_rgs_df.groupby("Read_ID")["aln_len"].transform('max')
self.P_rgs_df["log_P"] = self.P_rgs_df["log_P"] * self.P_rgs_df["max_aln_len"] / self.P_rgs_df["aln_len"]
Expand Down
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