SYNOPSIS

LAshow [-caroUF] [-iint(4)] [-wint(100)][-bint(10)] src1:db|dam [src2:db|dam] align:las [reads:FILE | reads:range ... ]

DESCRIPTION

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.

OPTIONS

-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.