Masai output - paired end mode synopsis masai_output_pe [options] genome file reads file l reads file r raw file l raw file r description masai is a fast and accurate read mapper based on approximate seeds and multiple backtracking. see http://www.seqan.de/projects/masai for more information. (c) copyright 2011-2012 by enrico siragusa. -h, --help displays this help message. --version display version information pairing options: -ng, --no-gaps do not align reads with gaps. -ll, --library-length num library length. default: 220. -le, --library-error num library length tolerance. default: 50. output options: -t, --tmp-folder str specify a huge temporary folder. default: use the genome folder. -o, --output-file file specify an output file. default: use the reads filename prefix. valid filetypes are: raw and sam. -nc, --no-cigar do not output cigar string. this only affects sam output. debug options: -nd, --no-dump do not dump results. version masai_output_pe version: 0.7.1 [14053] last update 2013-05-16