1TOOL="../../../OUTDIR/sra-tools/linux/gcc/x86_64/dbg/bin/vdb-sql" 2ACC="SRR341578" 3 4#COLS="READ;READ_LEN" 5#CREATE="create virtual table VDB using vdb( $ACC, columns=$COLS );" 6#CREATE="create virtual table VDB using vdb( $ACC, exclude=NAME );" 7CREATE="create virtual table VDB using vdb( $ACC );" 8 9 10#SELECT="select READ, READ_START, json_extract( json_object( 'a', READ_START ), '$.a[1]' ) from VDB limit 3;" 11 12#SELECT="select READ, READ_START, json_extract( json_object( 'a', json( READ_START ) ), '$.a[1]' ) from VDB limit 3;" 13 14#SELECT="select json_each.value, count( json_each.value ) from VDB, json_each( VDB.READ_FILTER ) group by json_each.value;" 15 16SELECT="select * from VDB limit 1;" 17 18#to prevent the shell from expanding '*' into filenames! 19set -f 20 21#CMD="$TOOL -line :memory: \"$CREATE $SELECT\"" 22#CMD="$TOOL -line -acc $ACC :memory: \"$SELECT\"" 23#echo $CMD 24#eval $CMD 25 26 27TMPFILE=`mktemp -u` 28 29#create a virtual table named FASTQ on our accession 30echo "create virtual table NGS using ngs( $ACC, style = PILEUP, ref = NC_011748.1 );" >> $TMPFILE 31#echo ".mode line" >> $TMPFILE 32#get something out of it... 33echo "select * FROM NGS WHERE DEPTH > 130;" >> $TMPFILE 34 35$TOOL < $TMPFILE 36 37rm $TMPFILE 38