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chore(call): more locus call process logging
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davidlougheed committed Jun 10, 2024
1 parent 51e37c3 commit ca21c35
Showing 1 changed file with 4 additions and 0 deletions.
4 changes: 4 additions & 0 deletions strkit/call/call_locus.py
Original file line number Diff line number Diff line change
Expand Up @@ -827,6 +827,8 @@ def call_locus(
)
call_dict_base["ref_cn"] = ref_cn # tag call dictionary with ref_cn

logger_.debug(f"{locus_log_str} - got ref. copy number: {ref_cn} ({l_offset=}; {r_offset=})")

# If our reference repeat count getter has altered the TR boundaries a bit (which is done to allow for
# more spaces in which an indel could end up), adjust our coordinates to match.
# Currently, contractions of the TR region are ignored.
Expand Down Expand Up @@ -861,6 +863,8 @@ def call_locus(
) = bf.get_overlapping_segments_and_related_data(
read_contig, left_flank_coord, right_flank_coord, max_reads, logger_, locus_log_str)

logger_.debug(f"{locus_log_str} - got {n_overlapping_reads} overlapping aligned segments")

if n_overlapping_reads > params.max_reads:
logger_.warning(f"{locus_log_str} - skipping locus; too many overlapping reads")
return call_dict_base
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