From ca21c35fea14a622f4c3875bdc795d0e8788f754 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 10 Jun 2024 09:01:58 -0400 Subject: [PATCH] chore(call): more locus call process logging --- strkit/call/call_locus.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/strkit/call/call_locus.py b/strkit/call/call_locus.py index ff4d30a..6b30d8d 100644 --- a/strkit/call/call_locus.py +++ b/strkit/call/call_locus.py @@ -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. @@ -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