fasta=$(lightning vcf2fasta -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf}) ; echo fasta=${fasta}
# fasta=su92l-4zz18-9nq05jifgz7iult
-ref37_lib=$(lightning import -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -include-no-calls ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
+ref37_lib=$(lightning import -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
# ref37_lib=su92l-4zz18-vnhlv3g6yp1azls/library.gob
# 539s
-ref38_lib=$(lightning import -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -include-no-calls ${ref_fa}) ; echo ref38_lib=${ref38_lib}
+ref38_lib=$(lightning import -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles ${ref_fa}) ; echo ref38_lib=${ref38_lib}
+# ref38_lib=su92l-4zz18-swebknshfwsvys6/library.gob
unfiltered=$(lightning import -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true ${fasta}) ; echo unfiltered=${unfiltered}
# unfiltered=su92l-4zz18-mz3546bib6oj1gg/library.gob
+# unfiltered=su92l-4zz18-72ovi5qrderxudv/library.gob
+# 24674s @ pre-38e6e7c
+# unfiltered=su92l-4zz18-ywhkc1hgdzxwp5u/library.gob
+# 18497s @ 64vcpu bf0968a
+# _____s @ 32vcpu 83983ad
+
merged=$(lightning merge -project ${project} -priority ${priority} ${unfiltered} ${ref37_lib}) ; echo merged=${merged}
# merged=su92l-4zz18-svw5xqe5g0ct2v1/library.gob
# exportvcf=su92l-4zz18-gz4svr6zyvipueu/export.csv
# 5506s
+exporthgvs=$(lightning export -project ${project} -priority ${priority} -i ${merged38} -output-format hgvs -ref /mnt/su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz -output-bed hg38.bed) ; echo exporthgvs=${exporthgvs}
+#
+#
+
stats=$(lightning stats -project ${project} -priority ${priority} -i ${merged}) ; echo stats=${stats}
filtered=$(lightning filter -project ${project} -priority ${priority} -i ${merged} -min-coverage "0.9" -max-variants "30") ; echo filtered=${filtered}
-annotations=$(lightning annotate -project ${project} -priority ${priority} -i ${merged}) ; echo annotated=${annotated}
+annotations=$(lightning annotate -project ${project} -priority ${priority} -i ${merged}) ; echo annotations=${annotations}
pca=$(lightning pca-go -project ${project} -priority ${priority} -i ${filtered} -one-hot) ; echo pca=${pca}
plot=$(lightning plot -project ${project} -priority ${priority} -i ${pca} -labels-csv ${info}/sample_info.csv -sample-fasta-dir ${fasta})
echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
echo ${plot%%/*}
-numpy=$(lightning export-numpy -project ${project} -priority ${priority} -i ${filtered} -one-hot)
+
+merged38=$(lightning merge -project ${project} -priority ${priority} ${unfiltered} ${ref38_lib}) ; echo merged38=${merged38}
+# merged38=su92l-4zz18-xq17gtaltjxbm3n/library.gob
+# 1602s
+# merged38=su92l-4zz18-5kcaci3hqzukjv2/library.gob
+# 2815s @ 83983ad
+
+numpy=$(lightning export-numpy -project ${project} -priority ${priority} -i ${merged38}) ; echo numpy=${numpy}
+# numpy=su92l-4zz18-w3dx5k79mtbz6qt/matrix.npy
+# 6155s
+# pcapy=$(lightning pca -project ${project} -priority ${priority} -i ${numpy}) ; echo pcapy=${pcapy}
+comvar=$(lightning numpy-comvar -project ${project} -priority ${priority} -i ${numpy} -annotations ${numpy%/matrix.npy}/annotations.tsv) ; echo comvar=${comvar}
+# comvar=su92l-4zz18-s1yhngobdvcoc2e/commonvariants.csv