Provided by: daligner_1.0+20151214-1_amd64
LAshow - display local alignments from .las files
LAshow [-caroUF] [-iint(4)] [-wint(100)][-bint(10)] src1:db|dam [src2:db|dam] align:las [reads:FILE | reads:range ... ]
LAshow produces a printed listing of the local alignments contained in the specified .las file, where the a- and b-reads come from src1 or from src1 and src2, respectively. If a file or list of read ranges is given, then only the overlaps for which the a-read is in the set specified by the file or list are displayed. See DBshow(1) for an explanation of how the file and list of read ranges are interpreted.
-F Reverse the roles of the a- and b- reads in the display -U Use uppercase for DNA sequence instead of the default lowercase -iindentation Set the indent for the cartoon and/or alignment displays if they are requested. (default: 4) -bnum_symbols Set the number of symbols on either side of the aligned segments in an alignment display. (default: 10) -ww This parameter is used for the display modes specified by -a and -r. (default: 100) -o Only display alignments that are proper overlaps-- that is, where a sequence end occurs at each end of the alignment DISPLAY MODES -c Cartoon rendering of the alignment -a, -r Display an alignment of the local alignment The -a option puts exactly w columns per segment of the display, whereas the -r option puts exactly w a-read symbols in each segment of the display. The -r display mode is useful when one wants to visually compare two alignments involving the same a-read. If a combination of the -c, -a, and -r flags is set, then the cartoon comes first, then the -a alignment, and lastly the -r alignment.