Masai output - single end mode synopsis masai_output_se [options] genome file reads file raw file 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 mapping options: -ng, --no-gaps do not align reads with gaps. -m, --matches num maximum number of matches per read. 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_se version: 0.7.1 [14053] last update 2013-05-16