Man page - existdb(1)

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Package: meryl
apt-get install meryl

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meryl

Manual

EXISTDB

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO

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 .