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existDB - Online in the Cloud

Run existDB in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command existDB that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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.

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