X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/b8a880e77baeeefe25f2b979070199fd750b58e8..67852718f3bad4936e271adcce9e59c03bdf9344:/example-su92l-1kg.sh

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
index 4bf721c55c..abb696440d 100755
--- a/example-su92l-1kg.sh
+++ b/example-su92l-1kg.sh
@@ -19,14 +19,21 @@ genome=$(lightning     ref2genome   -project ${project} -priority ${priority} -r
 fasta=$(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
@@ -36,6 +43,10 @@ exportvcf=$(lightning  export       -project ${project} -priority ${priority} -i
 # 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}
@@ -47,4 +58,16 @@ plot=$(lightning       plot         -project ${project} -priority ${priority} -i
 echo >&2 "https://workbench2.${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