NAME

       Raptor-upgrade  - A fast and space-efficient pre-filter for querying very large collections of nucleotide
       sequences.

SYNOPSIS

       raptor upgrade --input <file> --output <file> [--fpr <number>|--bins <file>]

DESCRIPTION

       Upgrades a Raptor index created with Raptor 2.0 to be compatible with Raptor 3.0.

       The only new parameter need is the false positive rate.  The  false  positive  rate  affects  the  search
       results. This can be done in three different ways:

       1) Pass the false positive rate via --fpr.

       2)  The  false  positive rate can be automatically determined if the paths of the files used to build the
       index are still available.

       3) Pass a file containing the path to the original files, one line per file. The false positive rate  can
       then  be  automatically determined. The order of the files does not matter. The file with the most k-mers
       will determine the false positive rate.

OPTIONS

       --fpr (double)
              The false positive rate. Mutually exclusive with --bins. Default: None. Value  must  be  in  range
              [0.000000,1.000000].

       --bins (std::filesystem::path)
              File containing one file per line per bin. Mutually exclusive with --fpr. Default: None. The input
              file must exist and read permissions must be granted.

       --input (std::filesystem::path)
              The index to upgrade. Parts: Without suffix _0

       --output (std::filesystem::path)
              Path to new index.

   Common options
       -h, --help
              Prints the help page.

       -hh, --advanced-help
              Prints the help page including advanced options.

       --version
              Prints the version information.

       --copyright
              Prints the copyright/license information.

       --export-help (std::string)
              Export the help page information. Value must be one of [html, man, ctd, cwl].

EXAMPLES

       raptor upgrade --input old.index --output new.index

       raptor upgrade --input old.index --output new.index --fpr 0.05

       raptor upgrade --input old.index --output new.index --bins bins.list

VERSION

       Last update: Unavailable
       Raptor-upgrade version: 3.0.1 (commit unavailable)
       Sharg version: 1.1.1
       SeqAn version: 3.3.0-rc.2

URL

       https://github.com/seqan/raptor

LEGAL

       Raptor-upgrade Copyright: BSD 3-Clause License
       Author: Enrico Seiler
       Contact: enrico.seiler@fu-berlin.de
       SeqAn Copyright: 2006-2023 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
       In your academic works please cite: Raptor: A fast and space-efficient pre-filter for querying very large
       collections  of  nucleotide  sequences; Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, and
       Knut Reinert; iScience 2021 24 (7): 102782. doi: https://doi.org/10.1016/j.isci.2021.102782
       For full copyright and/or warranty information see --copyright.

raptor-upgrade 3.0.1 (commit unavailable)          Unavailable                                 RAPTOR-UPGRADE(1)