incomplete download of pgx-main

pgx-main/test_files/test_cyp2d6.alleles

@@ -1,22 +0,0 @@
---------------------------------------------
-
-CYP2D6 Star Allele Calling with StellarPGx
-
---------------------------------------------
-
-Initially computed CN = 1
-
-Sample core variants:
-42126611~C>G~1/1;42127526~C>T~1/1;42128945~C>T~1/1;42129809~T>C~1/1;42129819~G>T~1/1;42130692~G>A~1/1
-
-Candidate alleles:
-['4.v7_4.v7']
-
-Result:
-*5/*4
-
-Activity score:
-0.0
-
-Metaboliser status:
-Poor metaboliser (PM)

pgx-main/test_files/test_cyp2d6.tsv

@@ -1 +0,0 @@
-CYP2D6	*5/*4

pgx-main/test_files/test_samples.txt

@@ -1,14 +0,0 @@
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-11B-20Dec2022_S27.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-12B-20Dec2022_S28.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-13B-20Dec2022_S24.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-15A-bravo_S20.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-16B-20Dec2022_S25.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-18A-bravo_S18.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-1B-bravo_S17.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-2A-bravo_S21.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-2B-bravo_S22.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-3A-bravo_S19.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-3B-bravo_S23.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-8A-20Dec2022_S26.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-NA12878-20Dec2022_S29.vcf
-s3://quantgene-portland-pgx/20230124-sp-pl42-hs2/pgx-pl42-dev0030/pgx-NA12878-3-bravo_S16.vcf