LICENSE.txt
MANIFEST.in
README.rst
setup.py
scripts/alignSampleToReference.sh
scripts/copy_snppipeline_data.py
scripts/create_snp_matrix.py
scripts/prepReference.sh
scripts/prepSamples.sh
snp_pipeline.egg-info/PKG-INFO
snp_pipeline.egg-info/SOURCES.txt
snp_pipeline.egg-info/dependency_links.txt
snp_pipeline.egg-info/requires.txt
snp_pipeline.egg-info/top_level.txt
snppipeline/__init__.py
snppipeline/snppipeline.py
snppipeline/utils.py
snppipeline/data/lambdaVirusExpectedResults/snplist.txt
snppipeline/data/lambdaVirusExpectedResults/snpma.fasta
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/reads.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/var.flt.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/reads.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/var.flt.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/reads.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/var.flt.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/reads.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/var.flt.vcf
snppipeline/data/lambdaVirusInputs/reference/lambda_virus.fasta
snppipeline/data/lambdaVirusInputs/samples/sample1/sample1_1.fastq
snppipeline/data/lambdaVirusInputs/samples/sample1/sample1_2.fastq
snppipeline/data/lambdaVirusInputs/samples/sample2/sample2_1.fastq
snppipeline/data/lambdaVirusInputs/samples/sample2/sample2_2.fastq
snppipeline/data/lambdaVirusInputs/samples/sample3/sample3_1.fastq
snppipeline/data/lambdaVirusInputs/samples/sample3/sample3_2.fastq
snppipeline/data/lambdaVirusInputs/samples/sample4/sample4_1.fastq
snppipeline/data/lambdaVirusInputs/samples/sample4/sample4_2.fastq
test/test_snppipeline.py
test/test_utils.py