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fix: gcnv wrapper regex curly-brackets parsed by python string formatting (#489 ) #501

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merged 9 commits into from
Apr 15, 2024
Merged

fix: gcnv wrapper regex curly-brackets parsed by python string formatting (#489 ) #501

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5cd358c
fix: adaptd contig_priors to used contig name style (#489)
Nicolai-vKuegelgen Feb 16, 2024
4e69c88
fixing
Nicolai-vKuegelgen Feb 16, 2024
221ed8b
Add fix for hardcoded X/Y contig names in gcnv/post_germline_calls
Nicolai-vKuegelgen Feb 23, 2024
1326f62
fix post_germline_calls_case_mode
Nicolai-vKuegelgen Feb 23, 2024
47366a1
fix typo
Nicolai-vKuegelgen Feb 26, 2024
3fa2be7
Adjustments based on code review
Nicolai-vKuegelgen Apr 8, 2024
20f7df4
Fix regex curly brackets being parsed by python string formatting
Nicolai-vKuegelgen Apr 15, 2024
c97db73
Merge branch 'main' into 489-gcnv-ploidy_priors-has-hard-coded-contig…
Nicolai-vKuegelgen Apr 15, 2024
ef24b4e
fix linting
Nicolai-vKuegelgen Apr 15, 2024
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2 changes: 1 addition & 1 deletion snappy_wrappers/wrappers/gcnv/contig_ploidy/wrapper.py
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Expand Up @@ -44,7 +44,7 @@
export THEANO_FLAGS="base_compiledir=$TMPDIR/theano_compile_dir"

# Get contig name style
egrep "^@SQ\s+SN:chr[0-9XY]{1,2}\s+" {snakemake.input.interval_list} > /dev/null && true
egrep "^@SQ\s+SN:chr[0-9XY]{{1,2}}\s+" {snakemake.input.interval_list} > /dev/null && true
exit_status=$?
if [[ $exit_status == 0 ]]; then
STYLE="chr"
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2 changes: 1 addition & 1 deletion snappy_wrappers/wrappers/gcnv/post_germline_calls/wrapper.py
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Expand Up @@ -28,7 +28,7 @@
# Get contig name style
# Note: the sample_index in '{snakemake.input.ploidy}' and '{snakemake.input.calls[0]}' are NOT guaranteed to be the same
# -> Sample_0 should always exist and the contig names (which we care for) are the same
tail -n +2 $(dirname {snakemake.input.ploidy})/ploidy-calls/SAMPLE_0/contig_ploidy.tsv | egrep "^chr[0-9XY]{1,2}\s[0-9]\s[0-9.]+" > /dev/null && true
tail -n +2 $(dirname {snakemake.input.ploidy})/ploidy-calls/SAMPLE_0/contig_ploidy.tsv | egrep "^chr[0-9XY]{{1,2}}\s[0-9]\s[0-9.]+" > /dev/null && true
exit_status=$?
if [[ $exit_status == 0 ]]; then
STYLE="chr"
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2 changes: 1 addition & 1 deletion snappy_wrappers/wrappers/gcnv/post_germline_calls_case_mode/wrapper.py
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Expand Up @@ -30,7 +30,7 @@
fi

# Get contig name style; SAMPLE_0 is guaranteed to exist
tail -n +2 $(dirname {snakemake.input.ploidy})/ploidy-calls/SAMPLE_0/contig_ploidy.tsv | grep "^chr[0-9XY]{1,2}\s[0-9]\s[0-9.]+$" > /dev/null && true
tail -n +2 $(dirname {snakemake.input.ploidy})/ploidy-calls/SAMPLE_0/contig_ploidy.tsv | grep "^chr[0-9XY]{{1,2}}\s[0-9]\s[0-9.]+$" > /dev/null && true
exit_status=$?
if [[ $exit_status == 0 ]]; then
STYLE="chr"
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