generate more test data setup from real data

jass/test/update_test_hdf5_files.sh

@@ -25,7 +25,13 @@ for DATA_DIR in $DATA_DIRS; do
   echo "Creating inittable"
   jass create-inittable --input-data-path "./${DATA_DIR}/z*.txt" --init-covariance-path "./${DATA_DIR}/COV.csv" --init-genetic-covariance-path ${GEN_COV} --regions-map-path "./${DATA_DIR}/regions.txt" --description-file-path "./${DATA_DIR}/summary.csv" --init-table-metadata-path "./${DATA_DIR}/metadata.txt" --init-table-path "./${DATA_DIR}/initTable.hdf5"
 
+  echo "Creating inittable without pre-computed covariance matrix"
+  jass create-inittable --input-data-path "./${DATA_DIR}/z*.txt"                                                --init-genetic-covariance-path ${GEN_COV} --regions-map-path "./${DATA_DIR}/regions.txt" --description-file-path "./${DATA_DIR}/summary.csv" --init-table-metadata-path "./${DATA_DIR}/metadata.txt" --init-table-path "./${DATA_DIR}/initTable-computed-cov.hdf5"
+
+  echo "Creating worktable with Nan"
+  jass create-project-data --init-table-path "${DATA_DIR}/initTable.hdf5" --phenotype ${TRAITS} --worktable-path ./${DATA_DIR}/worktable-withnans.hdf5
+
   echo "Creating worktable"
-  jass create-project-data --init-table-path "${DATA_DIR}/initTable.hdf5" --phenotype ${TRAITS} --worktable-path ./${DATA_DIR}/worktable.hdf5
+  jass create-project-data --init-table-path "${DATA_DIR}/initTable.hdf5" --phenotype ${TRAITS} --worktable-path ./${DATA_DIR}/worktable-nonans.hdf5 --remove-nans
 
 done
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