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ilyasoifer wants to merge 5 commits into from
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updated environment #256

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8013dd7
updated environment
ilyasoifer Jan 15, 2026
4dbdef1
update env
ilyasoifer Jan 15, 2026
e266070
fixed a minor bug in report
ilyasoifer Jan 16, 2026
8c3b412
Fixed no gt report
ilyasoifer Jan 17, 2026
8d2a4d6
updated submodule
ilyasoifer Jan 18, 2026
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10 changes: 7 additions & 3 deletions setup/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -62,12 +62,12 @@ dependencies:
- bzip2=1.0.8=h4bc722e_7
- c-ares=1.34.3=hb9d3cd8_1
- c-blosc2=2.15.2=h68e2383_0
- ca-certificates=2025.8.3=hbd8a1cb_0
- ca-certificates=2026.1.4=hbd8a1cb_0
- cached-property=1.5.2=hd8ed1ab_1
- cached_property=1.5.2=pyha770c72_1
- cachetools=5.5.0=pyhd8ed1ab_0
- cairo=1.18.0=hebfffa5_3
- certifi=2025.8.3=pyhd8ed1ab_0
- certifi=2026.1.4=pyhd8ed1ab_0
- cffi=1.17.1=py310h8deb56e_0
- cfgv=3.3.1=pyhd8ed1ab_0
- chardet=5.2.0=py310hff52083_2
Expand Down Expand Up @@ -181,6 +181,8 @@ dependencies:
- keyutils=1.6.1=h166bdaf_0
- kiwisolver=1.4.7=py310h3788b33_0
- krb5=1.21.3=h659f571_0
- k8=1.2=he8db53b_6
- kmc=3.2.4=h5ca1c30_4
- lame=3.100=h166bdaf_1003
- lcms2=2.16=hb7c19ff_0
- ld_impl_linux-64=2.43=h712a8e2_2
Expand Down Expand Up @@ -284,6 +286,7 @@ dependencies:
- matplotlib-base=3.7.1=py310he60537e_0
- matplotlib-inline=0.1.7=pyhd8ed1ab_0
- methyldackel=0.6.1=he4a0461_7
- minimap2=2.30=h577a1d6_0
- mistune=3.0.2=pyhd8ed1ab_0
- mock=5.1.0=pyhd8ed1ab_0
- mpg123=1.32.9=hc50e24c_0
Expand Down Expand Up @@ -311,7 +314,7 @@ dependencies:
- numpy=1.26.4=py310hb13e2d6_0
- openjdk=17.0.13=he018374_0
- openjpeg=2.5.2=h488ebb8_0
- openssl=3.5.2=h26f9b46_0
- openssl=3.6.0=h26f9b46_0
- orc=2.0.3=he039a57_0
- overrides=7.7.0=pyhd8ed1ab_0
- packaging=24.2=pyhff2d567_1
Expand Down Expand Up @@ -402,6 +405,7 @@ dependencies:
- seaborn-base=0.13.2=pyhd8ed1ab_2
- sed=4.8=he412f7d_0
- send2trash=1.8.3=pyh0d859eb_0
- seqkit=2.12.0=he881be0_1
- setuptools=75.6.0=pyhff2d567_1
- shap=0.46.0=cpu_py310h377a755_1
- sip=6.7.12=py310hc6cd4ac_0
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2 changes: 1 addition & 1 deletion ugbio_utils
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Submodule ugbio_utils updated 124 files
2 changes: 1 addition & 1 deletion ugvc/pipelines/run_no_gt_report.py
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Expand Up @@ -94,7 +94,7 @@ def snp_statistics(df, ref_fasta):
df = annotation.get_motif_around(df, 5, ref_fasta)
df = df.set_index(["chrom", "pos"])

df["af"] = df["af"].apply(lambda x: x[0])
df["af"] = df["af"].apply(lambda x: x[0] if isinstance(x, tuple) else x)
df["alt_1"] = df["alleles"].apply(lambda x: x[1])
df["alt_2"] = df["alleles"].apply(lambda x: x[2] if len(x) > 2 else None)

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2 changes: 1 addition & 1 deletion ugvc/reports/report_wo_gt.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -1113,7 +1113,7 @@
" if \"vaf\" in vcf_df.columns:\n",
" vcf_df[\"af\"] = vcf_df[\"vaf\"]\n",
"\n",
" vcf_df['af'] = vcf_df['af'].apply(lambda x: x[0])"
" vcf_df['af'] = vcf_df['af'].apply(lambda x: x[0] if isinstance(x, tuple) else x)"
]
},
{
Expand Down