.\" Automatically generated by Pod::Man 2.22 (Pod::Simple 3.07) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. 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Of course, you'll have to process the .\" output yourself in some meaningful fashion. .ie \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . nr % 0 . rr F .\} .el \{\ . de IX .. .\} .\" .\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2). .\" Fear. Run. Save yourself. 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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" mbfa \- Murasaki Binary FASTA format converter .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 1 \& mbfa [options...] [input] [input2 ...] #convert [input] and [input2 ...] to Muraaski Binary FASTA files .Ve .SH "DESCPRIPTION" .IX Header "DESCPRIPTION" Murasaki processes sequence data using a 2\-bit format where each base is reprsented using 2 bits. There's a number of pre-existing formats that do similar things, however in particular Murasaki needs to know about the metadata that can't be expressed in just 2 bits (eg. where sequences of NNNNs are, sequence breaks when multiple sequences are included in a \s-1FASTA\s0 file, etc.), therefore the \s-1MBFA\s0 format includes this data as well. Ordinarily these files are generated automatically by Murasaki when first run on a new sequence. .PP Because the file format is designed mesh closely with Murasaki, the actual file extension will vary to reflect your architecture. It will generally be some form of .mbfa[48][48] (e.g. \f(CW\*(C`.mbfa88\*(C'\fR (the default gcc build on an amd64)). .SH "OPTIONS" .IX Header "OPTIONS" .IP "\-\-info|\-i" 4 .IX Item "--info|-i" Show metadata about each \s-1MBFA\s0 specified. .IP "\-\-force|\-f" 4 .IX Item "--force|-f" By default \fBmbfa\fR will skip files that already have recent .mbfa files. This option forces the regeneration of these files. .IP "\-\-fatal|\-F" 4 .IX Item "--fatal|-F" Makes errors fatal. Ordinarily if you specify multiple files, mbfa will try to convert all of them even if one fails emitting a warning. With \-\-fatal it will stop and exit with an error if there's a problem. .IP "\-\-fasta|\-A" 4 .IX Item "--fasta|-A" Geneates \s-1FASTA\s0 output corresponding based on the \s-1MBFA\s0 data to stdout. .IP "\-\-help|\-h, \-\-version|\-V, \-\-verbose|\-V" 4 .IX Item "--help|-h, --version|-V, --verbose|-V" What you'd expect. .SH "LICENSE" .IX Header "LICENSE" \&\s-1GNU\s0 General Public License, version 3 (GPLv3) .SH "AVAILABILITY" .IX Header "AVAILABILITY" .SH "AUTHOR" .IX Header "AUTHOR" Kris Popendorf .SH "SEE ALSO" .IX Header "SEE ALSO" \&\fImurasaki\fR\|(1), \fIgeneparse\fR\|(1)