LICENSE.txt
MANIFEST.in
README.rst
setup.cfg
setup.py
scripts/alignSampleToReference.sh
scripts/calculate_snp_distances.py
scripts/call_consensus.py
scripts/collectSampleMetrics.sh
scripts/combineSampleMetrics.sh
scripts/copy_snppipeline_data.py
scripts/create_snp_list.py
scripts/create_snp_matrix.py
scripts/create_snp_reference_seq.py
scripts/mergeVcf.sh
scripts/prepReference.sh
scripts/prepSamples.sh
scripts/run_snp_pipeline.sh
scripts/snp_filter.py
snp_pipeline.egg-info/PKG-INFO
snp_pipeline.egg-info/SOURCES.txt
snp_pipeline.egg-info/dependency_links.txt
snp_pipeline.egg-info/entry_points.txt
snp_pipeline.egg-info/requires.txt
snp_pipeline.egg-info/top_level.txt
snppipeline/__init__.py
snppipeline/call_consensus.py
snppipeline/call_sites.py
snppipeline/cfsan_snp_pipeline.py
snppipeline/collect_metrics.py
snppipeline/combine_metrics.py
snppipeline/command.py
snppipeline/data.py
snppipeline/distance.py
snppipeline/fastq.py
snppipeline/filter_regions.py
snppipeline/index_ref.py
snppipeline/job_runner.py
snppipeline/map_reads.py
snppipeline/merge_sites.py
snppipeline/merge_vcfs.py
snppipeline/pileup.py
snppipeline/qarrayrun.py
snppipeline/run.py
snppipeline/snp_matrix.py
snppipeline/snp_reference.py
snppipeline/utils.py
snppipeline/vcf_writer.py
snppipeline/data/agonaExpectedResults/metrics.tsv
snppipeline/data/agonaExpectedResults/referenceSNP.fasta
snppipeline/data/agonaExpectedResults/referenceSNP_preserved.fasta
snppipeline/data/agonaExpectedResults/snp_distance_matrix.tsv
snppipeline/data/agonaExpectedResults/snp_distance_matrix_preserved.tsv
snppipeline/data/agonaExpectedResults/snp_distance_pairwise.tsv
snppipeline/data/agonaExpectedResults/snplist.txt
snppipeline/data/agonaExpectedResults/snplist_preserved.txt
snppipeline/data/agonaExpectedResults/snpma.fasta
snppipeline/data/agonaExpectedResults/snpma.vcf
snppipeline/data/agonaExpectedResults/snpma_preserved.fasta
snppipeline/data/agonaExpectedResults/snpma_preserved.vcf
snppipeline/data/agonaExpectedResults/samples/ERR178926/consensus.fasta
snppipeline/data/agonaExpectedResults/samples/ERR178926/var.flt.vcf
snppipeline/data/agonaExpectedResults/samples/ERR178929/consensus.fasta
snppipeline/data/agonaExpectedResults/samples/ERR178929/var.flt.vcf
snppipeline/data/agonaExpectedResults/samples/SRR1566386/consensus.fasta
snppipeline/data/agonaExpectedResults/samples/SRR1566386/var.flt.vcf
snppipeline/data/agonaExpectedResults/samples/SRR2566901/consensus.fasta
snppipeline/data/agonaExpectedResults/samples/SRR2566901/var.flt.vcf
snppipeline/data/agonaExpectedResults/samples/SRR3664651/consensus.fasta
snppipeline/data/agonaExpectedResults/samples/SRR3664651/var.flt.vcf
snppipeline/data/agonaExpectedResults/samples/SRR3665129/consensus.fasta
snppipeline/data/agonaExpectedResults/samples/SRR3665129/var.flt.vcf
snppipeline/data/agonaInputs/sampleList
snppipeline/data/agonaInputs/sha256sumCheck
snppipeline/data/agonaInputs/reference/NC_011149.fasta
snppipeline/data/configuration/snppipeline.conf
snppipeline/data/lambdaVirusExpectedResults/metrics.tsv
snppipeline/data/lambdaVirusExpectedResults/referenceSNP.fasta
snppipeline/data/lambdaVirusExpectedResults/referenceSNP_preserved.fasta
snppipeline/data/lambdaVirusExpectedResults/snp_distance_matrix.tsv
snppipeline/data/lambdaVirusExpectedResults/snp_distance_matrix_preserved.tsv
snppipeline/data/lambdaVirusExpectedResults/snp_distance_pairwise.tsv
snppipeline/data/lambdaVirusExpectedResults/snp_distance_pairwise_preserved.tsv
snppipeline/data/lambdaVirusExpectedResults/snplist.txt
snppipeline/data/lambdaVirusExpectedResults/snplist_preserved.txt
snppipeline/data/lambdaVirusExpectedResults/snpma.fasta
snppipeline/data/lambdaVirusExpectedResults/snpma.vcf
snppipeline/data/lambdaVirusExpectedResults/snpma_preserved.fasta
snppipeline/data/lambdaVirusExpectedResults/snpma_preserved.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/consensus.fasta
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/consensus.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/consensus_preserved.fasta
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/consensus_preserved.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/metrics
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/var.flt.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/var.flt_preserved.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample1/var.flt_removed.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/consensus.fasta
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/consensus.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/consensus_preserved.fasta
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/consensus_preserved.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/metrics
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/var.flt.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/var.flt_preserved.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample2/var.flt_removed.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/consensus.fasta
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/consensus.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/consensus_preserved.fasta
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/consensus_preserved.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/metrics
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/var.flt.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/var.flt_preserved.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample3/var.flt_removed.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/consensus.fasta
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/consensus.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/consensus_preserved.fasta
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/consensus_preserved.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/metrics
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/reads.all.pileup
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/reads.sam
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/var.flt.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/var.flt_preserved.vcf
snppipeline/data/lambdaVirusExpectedResults/samples/sample4/var.flt_removed.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
snppipeline/data/listeriaExpectedResults/metrics.tsv
snppipeline/data/listeriaExpectedResults/referenceSNP.fasta
snppipeline/data/listeriaExpectedResults/referenceSNP_preserved.fasta
snppipeline/data/listeriaExpectedResults/snp_distance_matrix.tsv
snppipeline/data/listeriaExpectedResults/snp_distance_matrix_preserved.tsv
snppipeline/data/listeriaExpectedResults/snp_distance_pairwise.tsv
snppipeline/data/listeriaExpectedResults/snplist.txt
snppipeline/data/listeriaExpectedResults/snplist_preserved.txt
snppipeline/data/listeriaExpectedResults/snpma.fasta
snppipeline/data/listeriaExpectedResults/snpma_preserved.fasta
snppipeline/data/listeriaExpectedResults/samples/SRR1553725/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553739/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553740/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553750/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553756/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553764/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553773/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553774/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553779/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553784/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553788/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553791/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553792/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553796/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553797/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553798/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553804/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553816/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553820/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553821/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553826/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553827/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553840/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553850/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553851/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553855/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553856/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553866/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553867/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553871/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553882/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553906/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1553907/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1554256/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1554259/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556285/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556286/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556287/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556288/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556289/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556290/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556291/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556292/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556293/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556294/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556295/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556296/var.flt.vcf
snppipeline/data/listeriaExpectedResults/samples/SRR1556297/var.flt.vcf
snppipeline/data/listeriaInputs/sampleList
snppipeline/data/listeriaInputs/sha256sumCheck
snppipeline/data/listeriaInputs/reference/CFSAN023463.HGAP.draft.fasta
test/__init__.py
test/test_cfsan_snp_pipeline.py
test/test_doctests.py