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.gitignore
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.gitignore
.vscode
test_data
__pycache__
acgt_codec.py
chunk_cache
pm_io_allel.py
SNPGenie2_orchards.py
trash.txt
VCFclass.py
SNPGenie
Popoolation
npstat
dask-worker-space
cyvcf2-main
format.c
format.py
format.pyx
format.pxd
test_data/Mammalian
test_data/drosophilia
misc.note
.gitignore
pimaker-env
misc.txt
.fasta
A_Singapore_INFIMH-16-0019_2016_HA.fasta
A_Singapore_INFIMH-16-0019_2016_MP.fasta
A_Singapore_INFIMH-16-0019_2016_NA.fasta
A_Singapore_INFIMH-16-0019_2016_NP.fasta
A_Singapore_INFIMH-16-0019_2016_NS.fasta
A_Singapore_INFIMH-16-0019_2016_PA.fasta
A_Singapore_INFIMH-16-0019_2016_PB1.fasta
A_Singapore_INFIMH-16-0019_2016_PB2.fasta
chr3.gtf
Picture1.svg
results_A_Singapore_INFIMH-16-0019_2016_HA_sites.csv
results_A_Singapore_INFIMH-16-0019_2016_HA_summary_statistics.csv.gz
results_A_Singapore_INFIMH-16-0019_2016_MP_sites.csv
results_A_Singapore_INFIMH-16-0019_2016_MP_summary_statistics.csv.gz
results_A_Singapore_INFIMH-16-0019_2016_NA_sites.csv
results_A_Singapore_INFIMH-16-0019_2016_NA_summary_statistics.csv.gz
results_A_Singapore_INFIMH-16-0019_2016_NP_sites.csv
results_A_Singapore_INFIMH-16-0019_2016_NP_summary_statistics.csv.gz
results_A_Singapore_INFIMH-16-0019_2016_NS_sites.csv
results_A_Singapore_INFIMH-16-0019_2016_NS_summary_statistics.csv.gz
results_A_Singapore_INFIMH-16-0019_2016_PA_sites.csv
results_A_Singapore_INFIMH-16-0019_2016_PA_summary_statistics.csv.gz
results_A_Singapore_INFIMH-16-0019_2016_PB1_sites.csv
results_A_Singapore_INFIMH-16-0019_2016_PB1_summary_statistics.csv.gz
results_A_Singapore_INFIMH-16-0019_2016_PB2_sites.csv
results_A_Singapore_INFIMH-16-0019_2016_PB2_summary_statistics.csv.gz
qrcode.png
results_genes.csv
results_samples.csv
small_genome_pimaker.py
ST
toy_fasta.fasta
toy_gtf.gtf
toy_vcf.vcf
small_genome_pimaker.py
FST_formula.svg
benchmarks.txt
ST
toy_vcf.tsv
.gitignore
old_pimaker.py
benchmarks.txt
docstrings.py
note.py
run_snpgenie.sh
small_genome_pimaker.py
tests.py
.RData
.Rhistory
benchmark_results.tsv
benchmark_times.svg
benchmark.sh
benchmarks.tsv
log.txt
PiMaker.Rproj
pinpis.snp
TCGA.LUAD.mutect.0458c57f-316c-4a7c-9294-ccd11c97c2f9.DR-10.0.somatic.maf.gz
test_parameters.txt
test.syn_nonsyn.txt
test.syn_nonsyn.txt.params
two_samples.vcf.gz
two_samples.vcf.gz.csi
.Rproj.user/3398B80A/persistent-state
.Rproj.user/3398B80A/saved_source_markers
.Rproj.user/3398B80A/pcs/debug-breakpoints.pper
.Rproj.user/3398B80A/pcs/files-pane.pper
.Rproj.user/3398B80A/pcs/source-pane.pper
.Rproj.user/3398B80A/pcs/windowlayoutstate.pper
.Rproj.user/3398B80A/pcs/workbench-pane.pper
.Rproj.user/shared/notebooks/patch-chunk-names
original_SNPGenie2_code/dask_FST.py
original_SNPGenie2_code/dask_SNPGenie2.py
original_SNPGenie2_code/FST.py
original_SNPGenie2_code/SNPGenie2_edited.py
original_SNPGenie2_code/SNPGenie2.py
popoolation_1/calculate-dxy.pl
popoolation_1/mauve-parser.pl
popoolation_1/Variance-at-position.pl
popoolation_1/Variance-sliding.pl
popoolation_1/VarSliding2Flybase.pl
popoolation_1/VarSliding2Wiggle.pl
popoolation_1/basic-pipeline/convert-fastq.pl
popoolation_1/basic-pipeline/filter-pileup-by-gtf.pl
popoolation_1/basic-pipeline/identify-genomic-indel-regions.pl
popoolation_1/basic-pipeline/mask-sam-indelregions.pl
popoolation_1/basic-pipeline/output.file
popoolation_1/basic-pipeline/output.file.params
popoolation_1/basic-pipeline/subsample-pileup.pl
popoolation_1/basic-pipeline/test.snp
popoolation_1/basic-pipeline/trim-fastq.pl
popoolation_1/Modules/BasicUtility.pm
popoolation_1/Modules/FormatSNP.pm
popoolation_1/Modules/Pileup.pm
popoolation_1/Modules/PileupTripletSlider.pm
popoolation_1/Modules/PileupTripletWindowSlider.pm
popoolation_1/Modules/SynNonSyn.pm
popoolation_1/Modules/Test.pm
popoolation_1/Modules/VarianceExactCorrection.pm
popoolation_1/Modules/VarianceUncorrected.pm
popoolation_1/Modules/VarMath.pm
popoolation_1/Modules/VarMathClassical.pm
popoolation_1/Modules/Test/PileupParser.pm
popoolation_1/Modules/Test/TClassicalVariance.pm
popoolation_1/Modules/Test/TPileupTripletSliding.pm
popoolation_1/Modules/Test/TSynNonSyn.pm
popoolation_1/Modules/Test/Variance.pm
popoolation_1/Modules/tmp/VarMath_ndm.pm
popoolation_1/syn-nonsyn/codon-table.txt
popoolation_1/syn-nonsyn/create-syn-nonsynmatrix.pl
popoolation_1/syn-nonsyn/nsl_p1.txt
popoolation_1/syn-nonsyn/nsl_p6.txt
popoolation_1/syn-nonsyn/Syn-nonsyn-at-position.pl
popoolation_1/syn-nonsyn/Syn-nonsyn-sliding.pl
vcflib
README.md