NAME¶
existDB - management of existDB files
SYNOPSIS¶
existDB [
-mersize mersize]
-build some.fasta prefix
existDB -describe prefix
existDB -testfiles some.fasta prefix
existDB -testexistence some.fasta
existDB -testexhaustive some.fasta some.meryl
DESCRIPTION¶
This program is part of libkmer.
OPTIONS¶
- -mersize mersize
- Use the specified mersize when building existDB tables.
- -build some.fasta prefix
- Build an existDB on all mers in some.fasta and save the
tables into prefix.
- -describe prefix
- Reports the state of some existDB file.
- -testfiles some.fasta prefix
- Build an existDB table from some.fasta. Write that table to
disk. Load the table back. Compare that each mer in some.fasta is
present in all three existDB tables created earlier.
- -testexistence some.fasta
- Build an existDB table from some.fasta, check that every mer
in some.fasta can be found in the table. Does not guarantee that
every mer in the table is found in the file.
- -testexhaustive some.fasta some.meryl
- Build an existDB table from some.fasta, check _EVERY_ mer
for existence. Complain if a mer exists in the table but not in the
meryl(1) database. Assumes some.meryl is the mercount of
some.fasta.
SEE ALSO¶
meryl(1),
positionDB(1)