NAME

       LAdump - display daligner local alignments in a simple format

SYNOPSIS

       LAdump [-cdt] [-o] src1:db|dam [ src2:db|dam ] align:las [ reads:FILE | reads:range ...  ]

DESCRIPTION

       Like LAshow(1), LAdump allows one to display the local alignments (LAs) of a subset of the
       piles in an .las file and select which information to show about them.  The difference  is
       that  the information is written in a very simple "1-code" ASCII format that makes it easy
       for one to read and parse the information for further use.  For each LA the pair of  reads
       is  output  on  a  line.   -c  requests  that one further output the coordinates of the LA
       segments be output.  The -d option requests that the number of difference  in  the  LA  be
       output,  and  -t requests that the tracepoint information be output.  Finally, -o requests
       that only LAs that are proper overlaps be output.

       The format is very simple.  Each requested piece of information occurs  on  a  line.   The
       first  character  of every line is a "1-code" character that tells you what information to
       expect on the line.  The rest  of  the  line  contains  information  where  each  item  is
       separated  by  a single blank space.  The trace point line gives the number of trace point
       intervals in the LA and is immediately followed by that many lines containing  a  pair  of
       integers  giving  the  #  of differences and b-displacement in each successive trace point
       interval.

              P #a #b           - (#a,#b) have an LA between them
              C #ab #ae #bb #be - [#ab,#ae] aligns with [#bb,#be]
              D #               - there are # differences in the LA
              T #n              - there are #n trace point intervals for the LA
               (#d #y )^#n      - there are #d difference aligning the #y bp's of B with the
                                     next fixed-size interval of A
              + X #             - Total amount of X (X = P or T)
              % X #             - Maximum amount of X in any pile (X = P or T)
              @ T #             - Maximum number of trace points in any trace

       1-code lines that begin with +, %, or @ are always the first lines in  the  output.   They
       give  size information about what is contained in the output.  Specifically, '+ X #' gives
       the total number of LAs (X=P), or the total number of trace point intervals (X=T)  in  the
       file .  '% X #' gives the maximum number of LAs (X=P) or the maximum number of trace point
       intervals (X=T) in a given pile (collection of LAs all with the same a-read (applies  only
       to  sorted  Finally @ T # gives the maximum # of trace point intervals in any trace within
       the file.

SEE ALSO

       daligner(1)