Call 2-base deletion-insertion as two adjacent SNPs. refs #18496 refs #18438 Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Add -p-value and -cases options for exporting hgvs numpy. refs #17562 Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Add -match-genome=regexp filter. refs #17939 refs #17922 Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Export hgvs one-hot numpy: -1 for missing / low quality tiles. refs #17562 Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Add filter options to export cmd. refs #17562 Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Add copyright headers. Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Export hgvs one-hot numpy. Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Use tsv filename when using tab separator. Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Fix up VCF format. Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Separate pvcf/vcf output. Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Fix missing output. Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Option to export one vcf/csv file per chromosome. Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Write hgvs-based numpy matrix. Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Export hgvs-onehot. Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>