Index

Symbols

--batch_size oddSNP-cpsnpic-calculate-cpsnpic command line option oddSNP-cpsnpic-run-all command line option --celltag oddSNP-downsample-barcode-downsampling command line option oddSNP-downsample-reads-downsampling command line option oddSNP-utils-cslite-pileup command line option --force oddSNP-cpsnpic-calculate-cpsnpic command line option oddSNP-cpsnpic-generate-histogram command line option oddSNP-cpsnpic-run-all command line option oddSNP-cpsnpic-save-cpsnpic-plot command line option oddSNP-downsample-barcode-downsampling command line option oddSNP-downsample-reads-downsampling command line option oddSNP-downsample-vcf-downsampling command line option oddSNP-genotype-aggregate-pileup command line option oddSNP-snpic-calculate-snpic command line option oddSNP-snpic-estimate-donor-assignment command line option oddSNP-snpic-generate-histogram command line option oddSNP-snpic-run-all command line option oddSNP-snpic-save-donor-estimation-plot command line option oddSNP-snpic-save-snpic-plot command line option oddSNP-utils-cslite-pileup command line option oddSNP-utils-vireo command line option

--genotag oddSNP-utils-vireo command line option --genotype oddSNP-utils-vireo command line option --mincount oddSNP-utils-cslite-pileup command line option --ndonor oddSNP-utils-vireo command line option --nproc oddSNP-cpsnpic-calculate-cpsnpic command line option oddSNP-cpsnpic-run-all command line option oddSNP-downsample-barcode-downsampling command line option oddSNP-downsample-reads-downsampling command line option oddSNP-downsample-vcf-downsampling command line option oddSNP-utils-count-lines command line option oddSNP-utils-cslite-pileup command line option oddSNP-utils-vireo command line option --seed oddSNP-downsample-reads-downsampling command line option oddSNP-snpic-estimate-donor-assignment command line option --umitag oddSNP-utils-cslite-pileup command line option

A

AGFILE oddSNP-snpic-estimate-donor-assignment command line option oddSNP-snpic-generate-histogram command line option

assert_cellsnplite() (in module oddSNP.utils) assert_vireo() (in module oddSNP.utils)

B

BAM oddSNP-downsample-barcode-downsampling command line option oddSNP-downsample-reads-downsampling command line option oddSNP-utils-count-lines command line option oddSNP-utils-cslite-pileup command line option

BARCODES oddSNP-downsample-barcode-downsampling command line option oddSNP-utils-cslite-pileup command line option BARFILE oddSNP-snpic-estimate-donor-assignment command line option oddSNP-snpic-save-donor-estimation-plot command line option

C

call_aggregate_pileup() (in module oddSNP.genotype) call_barcode_downsampling() (in module oddSNP.downsampling) call_calculate_cpsnpic() (in module oddSNP.cpsnpic) call_calculate_snpic() (in module oddSNP.snpic) call_count_lines() (in module oddSNP.utils) call_cslite_pileup() (in module oddSNP.utils) call_estimate_donor_assignment() (in module oddSNP.snpic) call_generate_histogram() (in module oddSNP.cpsnpic) (in module oddSNP.snpic)

call_reads_downsampling() (in module oddSNP.downsampling) call_run_all() (in module oddSNP.cpsnpic) (in module oddSNP.snpic) call_save_cpsnpic_plot() (in module oddSNP.cpsnpic) call_save_donor_estimation_plot() (in module oddSNP.snpic) call_save_snpic_plot() (in module oddSNP.snpic) call_vcf_downsampling() (in module oddSNP.downsampling) call_vireo() (in module oddSNP.utils) CPFILE oddSNP-cpsnpic-generate-histogram command line option

G

generate_bam_index() (in module oddSNP.utils) generate_cpsnpic_plot() (in module oddSNP.plotting)

generate_donor_distribution_plot() (in module oddSNP.plotting) generate_snpic_plot() (in module oddSNP.plotting) generate_vcf_index() (in module oddSNP.utils)

H

HISTOFILE oddSNP-cpsnpic-save-cpsnpic-plot command line option oddSNP-snpic-save-snpic-plot command line option

I

INPATH oddSNP-cpsnpic-calculate-cpsnpic command line option oddSNP-cpsnpic-run-all command line option oddSNP-genotype-aggregate-pileup command line option oddSNP-snpic-calculate-snpic command line option oddSNP-snpic-run-all command line option oddSNP-utils-vireo command line option

M

matchingSNPs() (in module oddSNP.cpsnpic) module oddSNP.cpsnpic oddSNP.downsampling oddSNP.genotype oddSNP.plotting oddSNP.snpic oddSNP.utils

N

N oddSNP-snpic-estimate-donor-assignment command line option

O

oddSNP-cpsnpic-calculate-cpsnpic command line option --batch_size --force --nproc INPATH OUPATH oddSNP-cpsnpic-generate-histogram command line option --force CPFILE OUPATH oddSNP-cpsnpic-run-all command line option --batch_size --force --nproc INPATH OUPATH oddSNP-cpsnpic-save-cpsnpic-plot command line option --force HISTOFILE OUTPUT oddSNP-downsample-barcode-downsampling command line option --celltag --force --nproc BAM BARCODES OUPATH oddSNP-downsample-reads-downsampling command line option --celltag --force --nproc --seed BAM OUPATH READS oddSNP-downsample-vcf-downsampling command line option --force --nproc OUT REGIONS VCF oddSNP-genotype-aggregate-pileup command line option --force INPATH OUPATH oddSNP-snpic-calculate-snpic command line option --force INPATH OUPATH oddSNP-snpic-estimate-donor-assignment command line option --force --seed AGFILE BARFILE N OUPATH oddSNP-snpic-generate-histogram command line option --force AGFILE OUPATH oddSNP-snpic-run-all command line option --force INPATH OUPATH

oddSNP-snpic-save-donor-estimation-plot command line option --force BARFILE OUTPUT oddSNP-snpic-save-snpic-plot command line option --force HISTOFILE OUTPUT oddSNP-utils-count-lines command line option --nproc BAM oddSNP-utils-cslite-pileup command line option --celltag --force --mincount --nproc --umitag BAM BARCODES OUPATH REFERENCE oddSNP-utils-vireo command line option --force --genotag --genotype --ndonor --nproc INPATH OUPATH oddSNP.cpsnpic module oddSNP.downsampling module oddSNP.genotype module oddSNP.plotting module oddSNP.snpic module oddSNP.utils module OUPATH oddSNP-cpsnpic-calculate-cpsnpic command line option oddSNP-cpsnpic-generate-histogram command line option oddSNP-cpsnpic-run-all command line option oddSNP-downsample-barcode-downsampling command line option oddSNP-downsample-reads-downsampling command line option oddSNP-genotype-aggregate-pileup command line option oddSNP-snpic-calculate-snpic command line option oddSNP-snpic-estimate-donor-assignment command line option oddSNP-snpic-generate-histogram command line option oddSNP-snpic-run-all command line option oddSNP-utils-cslite-pileup command line option oddSNP-utils-vireo command line option OUT oddSNP-downsample-vcf-downsampling command line option OUTPUT oddSNP-cpsnpic-save-cpsnpic-plot command line option oddSNP-snpic-save-donor-estimation-plot command line option oddSNP-snpic-save-snpic-plot command line option

R

READS oddSNP-downsample-reads-downsampling command line option REFERENCE oddSNP-utils-cslite-pileup command line option

REGIONS oddSNP-downsample-vcf-downsampling command line option

S

save_plot() (in module oddSNP.plotting)

V

VCF oddSNP-downsample-vcf-downsampling command line option