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Always remove temporary VCF files #266

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Always remove temporary VCF files #266

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79dcdb4
readme fix
ThijsMaas Jul 5, 2024
e844a55
always remove temp vcf files
ThijsMaas Jul 5, 2024
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,7 @@ We can download some for you! InSilicoSeq can download random genomes from the n
The command

```shell
iss generate --ncbi bacteria -u 10 --model MiSeq --output ncbi_reads
iss generate --ncbi bacteria -U 10 --model MiSeq --output ncbi_reads
```

will generate 1 million reads from 10 random bacterial genomes.
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2 changes: 1 addition & 1 deletion iss/app.py
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Expand Up @@ -122,7 +122,7 @@ def generate_reads(args):
# and reads were appended to the same temp file.
temp_R1 = [temp_file + "_R1.fastq" for temp_file in temp_file_list]
temp_R2 = [temp_file + "_R2.fastq" for temp_file in temp_file_list]
temp_mut = [temp_file + ".vcf" for temp_file in temp_file_list] if args.store_mutations else []
temp_mut = [temp_file + ".vcf" for temp_file in temp_file_list]
util.concatenate(temp_R1, args.output + "_R1.fastq")
util.concatenate(temp_R2, args.output + "_R2.fastq")
if args.store_mutations:
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