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)

1.0                                                August 2015                                         LAshow(1)