maf_index - build and examine MAF indexes
maf_index [-t] maf index
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
maf_index can dump out the index data in human-readable
form for debugging.
The maf input file must be a valid MAF file of any length. It can optionally be BGZF-compressed, as produced by bgzip(1) from samtools.
The index created is a Kyoto Cabinet TreeDB (B+ tree) database;
index must have a
All sequences, not just the reference sequence, will be indexed for searching.
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
Print elapsed time for index creation. Mainly useful for measuring performance with different Ruby implementations, I/O subsystems, etc.
Run quietly, with warnings suppressed.
Run verbosely, with additional informational messages.
Log debugging information.
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
maf_index is a Ruby program and relies on ordinary Ruby environment
maf_index does not currently allow Kyoto Cabinet database parameters
to be set.
maf_index is copyright (C) 2012 Clayton Wheeler.
ruby(1), kctreemgr(1), bgzip(1)