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fahash

FAHASH(1)							   User Commands							 FAHASH(1)

NAME

       fahash - sequence hash builder for reverse e-PCR

SYNOPSIS

       fahash [-hV] -b hash-file [-w wdsize] [-f period] [-F fragment_min,fragment_max] [-k] [-c cachesize] [-v 1|2] famap-file ...

       fahash [-hV] -T hash-file [-o outfile]

DESCRIPTION

       The program fahash is part of the e-PCR suite and is used to build hash-files, and output word usage statistics for reverse e-PCR searches.

OPTIONS

       -b hash-file
	      Build hash tables (hash-file) from sequence files,

       -T hash-file
	      Print word usage statistics for hash-file

       -o outfile
	      Write output to file `outfile'

   build-options:
       -w wordsize
	      Set word size when building hash tables

       -f period
	      Set discontiguity when building hash tables

       -k     Skip repeats when building hash-file

       -F min,max
	      Set watermarks for fragment size (in Mb) (version 1 only)

       -c cachesize
	      Set cache size (version 2 only)

       -v ver Use format version (1|2, 2 is default)

EXAMPLE

	famap -tN -b genome.famap org/chr_*.fa

	fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap

	re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200

       See famap(1) and re-pcr(1)

SEE ALSO

       /usr/share/doc/ncbi-epcr/README.txt

       bioperl(1), e-pcr(1), famap(1) and re-pcr(1)

AUTHORS

       This  manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others).  Permission is granted
       to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
       the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

Reverse e-PCR: sequence hash builder version 2.3.9		    April 2008								 FAHASH(1)

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