LICENSE.txt
MANIFEST.in
README.rst
setup.py
scripts/alignSampleToReference.sh
scripts/copy_snppipeline_data.py
scripts/create_snp_list.py
scripts/create_snp_matrix.py
scripts/create_snp_pileup.py
scripts/create_snp_reference_seq.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/agonaExpectedResults/referenceSNP.fasta
snppipeline/data/agonaExpectedResults/snplist.txt
snppipeline/data/agonaExpectedResults/snpma.fasta
snppipeline/data/agonaExpectedResults/samples/ERR178926/reads.snp.pileup
snppipeline/data/agonaExpectedResults/samples/ERR178926/var.flt.vcf
snppipeline/data/agonaExpectedResults/samples/ERR178927/reads.snp.pileup
snppipeline/data/agonaExpectedResults/samples/ERR178927/var.flt.vcf
snppipeline/data/agonaExpectedResults/samples/ERR178928/reads.snp.pileup
snppipeline/data/agonaExpectedResults/samples/ERR178928/var.flt.vcf
snppipeline/data/agonaExpectedResults/samples/ERR178929/reads.snp.pileup
snppipeline/data/agonaExpectedResults/samples/ERR178929/var.flt.vcf
snppipeline/data/agonaExpectedResults/samples/ERR178930/reads.snp.pileup
snppipeline/data/agonaExpectedResults/samples/ERR178930/var.flt.vcf
snppipeline/data/agonaInputs/sha256sumCheck
snppipeline/data/agonaInputs/reference/NC_011149.fasta
snppipeline/data/lambdaVirusExpectedResults/referenceSNP.fasta
snppipeline/data/lambdaVirusExpectedResults/snplist.txt
snppipeline/data/lambdaVirusExpectedResults/snpma.fasta
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/reads.snp.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/var.flt.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/reads.snp.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/var.flt.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/reads.snp.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/var.flt.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/reads.snp.pileup
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