From 79dcdb46768e3f6d77ddf60ed3f0db42a66bbf40 Mon Sep 17 00:00:00 2001 From: Thijs Date: Fri, 5 Jul 2024 15:23:54 +0200 Subject: [PATCH 1/2] readme fix --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1a63e0c..c6f9b95 100644 --- a/README.md +++ b/README.md @@ -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. From e844a553f11f1e4cf6b60989d7c35e0b78c1703d Mon Sep 17 00:00:00 2001 From: Thijs Date: Fri, 5 Jul 2024 15:51:07 +0200 Subject: [PATCH 2/2] always remove temp vcf files --- iss/app.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/iss/app.py b/iss/app.py index bbcdbdd..f4d830e 100644 --- a/iss/app.py +++ b/iss/app.py @@ -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: