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maf_index(1) -- build and examine MAF indexes
=============================================
## SYNOPSIS
`maf_index` [-t] <maf> <index><br>
`maf_index` `-d`|`--dump` <index>
## DESCRIPTION
**maf_index** is part of the bioruby-maf library and creates
Kyoto Cabinet indexes for Multiple Alignment Format (MAF)
files. These indexes enable other MAF tools to selectively extract
alignment blocks of interest.
In its default mode, `maf_index` parses the <maf> file given as an
argument and creates an index in <index>.
The index data is stored in binary form, so with the `--dump`
argument, `maf_index` can dump out the index data in human-readable
form for debugging.
## FILES
The <maf> input file must be a valid MAF file of any length.
The index created is a Kyoto Cabinet TreeDB (B+ tree) database;
<index> must have a `.kct` extension.
## OPTIONS
TODO
* `-d`, `--dump`:
Instead of creating an index, dump out the given <index> in
human-readable form. Index records will appear like:
0 [bin 1195] 80082334:80082368
offset 16, length 1087
text size: 54
sequences in block: 10
species vector: 00000000000003ff
* `-t`, `--threaded`:
Use a separate reader thread to do I/O in parallel with
parsing. Only useful on JRuby.
* `--time`:
Print elapsed time for index creation. Mainly useful for measuring
performance with different Ruby implementations, I/O subsystems,
etc.
## EXAMPLES
Build an index on a MAF file:
$ maf_index chr22.maf chr22.kct
Dump out an index:
$ maf_index -d chr22.kct > /tmp/chr22.dump
## ENVIRONMENT
`maf_index` is a Ruby program and relies on ordinary Ruby environment
variables.
## BUGS
`maf_index` does not currently allow Kyoto Cabinet database parameters
to be set.
## COPYRIGHT
`maf_index` is copyright (C) 2012 Clayton Wheeler.
## SEE ALSO
ruby(1), kctreemgr(1)
* <https://github.com/csw/bioruby-maf/>
* <http://fallabs.com/kyotocabinet/>
Version data entries
6 entries across 6 versions & 1 rubygems