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LAdump - display daligner local alignments in a simple format


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


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

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.

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