SYNOPSIS
LAdump [cdt] [o] src1:dbdam [ src2:dbdam ] 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 "1code" 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 "1code" 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 bdisplacement 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 fixedsize 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
1code 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 aread (applies only to sorted Finally @ T # gives the maximum # of trace point intervals in any trace within the file.