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Minor update to star allele reporting
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xiao-chen-xc committed Apr 29, 2021
1 parent ac1602a commit 0031eeb
Showing 1 changed file with 12 additions and 12 deletions.
24 changes: 12 additions & 12 deletions star_caller.py
Original file line number Diff line number Diff line change
Expand Up @@ -395,19 +395,19 @@ def d6_star_caller(
)

genotype_filter = None
final_star_allele_call = None
# no-call due to star allele matching
if "no_match" in star_called[0]: # or star_called[0] == 'more_than_one_match':
final_star_allele_call = None
else:
final_star_allele_call = star_called[-1]
if ";" in final_star_allele_call:
genotype_filter = "More_than_one_possible_genotype"
elif "/" not in final_star_allele_call:
genotype_filter = "Not_assigned_to_haplotypes"
elif high_cn_low_confidence:
genotype_filter = "LowQ_high_CN"
else:
genotype_filter = "PASS"
if star_called.call_info and star_called.call_info != "no_match":
final_star_allele_call = star_called.clean_call
if final_star_allele_call:
if ";" in final_star_allele_call:
genotype_filter = "More_than_one_possible_genotype"
elif "/" not in final_star_allele_call:
genotype_filter = "Not_assigned_to_haplotypes"
elif high_cn_low_confidence:
genotype_filter = "LowQ_high_CN"
else:
genotype_filter = "PASS"

sample_call = d6_call(
normalized_depth.mad,
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