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Coerce SV ID type to str on VCF ingestion #12

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Coerce SV ID type to str on VCF ingestion #12

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4 changes: 3 additions & 1 deletion minda/decompose.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,7 @@ def get_df(vcf):
else:
df = pd.read_csv(vcf, comment='#', sep='\t', usecols=[0,1,2,4,6,7], header=None, compression='gzip', dtype={'#CHROM': 'str', 'POS':'Int64'})
df.columns = ['#CHROM', 'POS', 'ID', 'ALT', 'FILTER', 'INFO']
df['ID'] = df['ID'].astype('str')

return df

Expand All @@ -83,6 +84,7 @@ def get_intersected_df(vcf, bed):
intersect_obj = vcf_to_bt.intersect(bed_to_bt, u=True)
df = BedTool.to_dataframe(intersect_obj, header=None, usecols=[0,1,2,4,6,7], dtype={'#CHROM': 'str', 'POS':'int'})
df.columns = ['#CHROM', 'POS', 'ID', 'ALT', 'FILTER', 'INFO']
df['ID'] = df['ID'].astype('str')
return df


Expand Down Expand Up @@ -457,4 +459,4 @@ def get_decomposed_dfs(caller_name, df, filter, min_size, prefixed, vaf, sample_
decomposed_df_1.ID = prefix + "_" + decomposed_df_1['ID'].astype(str)
decomposed_df_2.ID = prefix + "_" + decomposed_df_2['ID'].astype(str)

return decomposed_df_1, decomposed_df_2, max_svlen
return decomposed_df_1, decomposed_df_2, max_svlen