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README

README

$Id$

Program			Function	
-------			--------
colourise		convert letterspace fasta files to colourspace
mergehits-cs		merge all hits into one line per read (colour space)
mergehits-ls		merge all hits into one line per read (letter space)
probcalc		parse rmapper output (non-pretty-printed output)
prettyprint-cs		pretty print alignments from rmapper/probcalc (c. space)
prettyprint-ls		pretty print alignments from rmapper/probcalc (l. space)
revcmpl			generate reverse complements of fasta reftigs
rmapper-cs		colourspace read mapper
rmapper-ls		letterspace read mapper
splitreads		split fasta read files into smaller chunks
splittigs		split fasta contig files into one file per contig
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