NAME

       LAshow - display local alignments from .las files

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.

SEE ALSO

       daligner(1)   LAsort(1)   LAmerge(1)   LAcat(1)   LAsplit(1)   LAcheck(1)   HPCdaligner(1)
       HPCmapper(1)