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.TH "MAF_INDEX" "1" "August 2012" "BioRuby" "BioRuby Manual"
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.SH "NAME"
\fBmaf_index\fR \- build and examine MAF indexes
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.SH "SYNOPSIS"
\fBmaf_index\fR [\-t] \fImaf\fR \fIindex\fR
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.br
\fBmaf_index\fR \fB\-d\fR|\fB\-\-dump\fR \fIindex\fR
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.SH "DESCRIPTION"
\fBmaf_index\fR 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\.
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.P
In its default mode, \fBmaf_index\fR parses the \fImaf\fR file given as an argument and creates an index in \fIindex\fR\.
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.P
The index data is stored in binary form, so with the \fB\-\-dump\fR argument, \fBmaf_index\fR can dump out the index data in human\-readable form for debugging\.
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.SH "FILES"
The \fImaf\fR input file must be a valid MAF file of any length\. It can optionally be BGZF\-compressed, as produced by bgzip(1) from samtools\.
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.P
The index created is a Kyoto Cabinet TreeDB (B+ tree) database; \fIindex\fR must have a \fB\.kct\fR extension\.
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.SH "OPTIONS"
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.TP
\fB\-a\fR, \fB\-\-all\fR
All sequences, not just the reference sequence, will be indexed for searching\.
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.TP
\fB\-d\fR, \fB\-\-dump\fR
Instead of creating an index, dump out the given \fIindex\fR in human\-readable form\. Index records will appear like:
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.IP "" 4
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.nf

 0 [bin 1195] 80082334:80082368
   offset 16, length 1087
   text size: 54
   sequences in block: 10
   species vector: 00000000000003ff
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.fi
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.IP "" 0

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.TP
\fB\-\-time\fR
Print elapsed time for index creation\. Mainly useful for measuring performance with different Ruby implementations, I/O subsystems, etc\.
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.TP
\fB\-q\fR, \fB\-\-quiet\fR
Run quietly, with warnings suppressed\.
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.TP
\fB\-v\fR, \fB\-\-verbose\fR
Run verbosely, with additional informational messages\.
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.TP
\fB\-\-debug\fR
Log debugging information\.
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.SH "EXAMPLES"
Build an index on a MAF file:
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.IP "" 4
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.nf

$ maf_index chr22\.maf chr22\.kct
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.fi
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.IP "" 0
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.P
Dump out an index:
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.IP "" 4
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.nf

$ maf_index \-d chr22\.kct > /tmp/chr22\.dump
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.fi
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.IP "" 0
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.SH "ENVIRONMENT"
\fBmaf_index\fR is a Ruby program and relies on ordinary Ruby environment variables\.
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.SH "BUGS"
\fBmaf_index\fR does not currently allow Kyoto Cabinet database parameters to be set\.
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.SH "COPYRIGHT"
\fBmaf_index\fR is copyright (C) 2012 Clayton Wheeler\.
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.SH "SEE ALSO"
ruby(1), kctreemgr(1), bgzip(1)
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.IP "\(bu" 4
\fIhttps://github\.com/csw/bioruby\-maf/\fR
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.IP "\(bu" 4
\fIhttp://fallabs\.com/kyotocabinet/\fR
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.IP "" 0