big test tuning

Author: mlin

loaders/vcf_into_sqlite.cc

@@ -618,7 +618,7 @@ void help() {
         << "Options: " << '\n'
         << "  --table-prefix PREFIX      prefix to the name of each table created" << '\n'
         << "  --ploidy N                 set max ploidy => # GT columns (default 2)" << '\n'
-        << "  --genotypes-without-rowid  make the genotypes table WITHOUT ROWID (advantageous if there are few/no FORMAT fields)"
+        << "  --genotypes-without-rowid  make the genotypes table WITHOUT ROWID (advantageous if the FORMAT fields aren't too large)"
         << '\n'
         << "  --no-gri                   skip genomic range indexing" << '\n'
         << "  -l,--level LEVEL           database compression level (-7 to 22, default 6)" << '\n'

test/genomicsqlite_big_tests.wdl

@@ -129,7 +129,7 @@ task test_sam {
 
         # add a QNAME-sorted seqs table
         chmod +x /usr/lib/python3.8/genomicsqlite.py
-        time /usr/lib/python3.8/genomicsqlite.py "~{dbname}" "CREATE TABLE reads_seqs_by_qname AS SELECT * from reads_seqs ORDER BY qname"
+        time /usr/lib/python3.8/genomicsqlite.py "~{dbname}" "CREATE TABLE reads_seqs_by_qname AS SELECT * from reads_seqs NOT INDEXED ORDER BY qname"
         >&2 ls -l "~{dbname}"
         time /usr/lib/python3.8/genomicsqlite.py "~{dbname}" "DROP TABLE reads_seqs_by_qname"
         >&2 ls -l "~{dbname}"
@@ -171,7 +171,7 @@ task test_vcf {
         chmod +x /usr/local/bin/vcf_into_sqlite
 
         # load database
-        time vcf_into_sqlite "~{variants}" "~{dbname}"
+        time vcf_into_sqlite --genotypes-without-rowid "~{variants}" "~{dbname}"
 
         # GRI query
         time python3 - <<"EOF"