cmpress1

Usage

Overview

Starting from a CM database <cmfile> in standard Infernal-1.1 format, construct binary compressed datafiles for cmscan. The cmpress step is required for cmscan to work.

The <cmfile> must be have already been calibrated with cmcalibrate for cmpress to work.

Four files are created: <cmfile>.i1m, <cmfile>.i1i, <cmfile>.i1f, and <cmfile>.i1p. The <cmfile>.i1m file contains the covariance models, associated filter p7 profile HMMs and their annotation in a binary format. The <cmfile>.i1i file is an SSI index for the <cmfile>.i1m file. The <cmfile>.i1f file contains precomputed data structures for the fast heuristic filter (the SSV filter) for the filter p7 profile HMMs in <cmfile>. The <cmfile>.i1p file contains precomputed data structures for the rest of each profile filter p7 HMM.

<cmfile> may not be '-' (dash); running cmpress on a standard input stream rather than a file is not allowed.

Options

-h

Help; print a brief reminder of command line usage and all available options.

-F

Force; overwrites any previous cmpress'ed datafiles. The default is to bitch about any existing files and ask you to delete them first.