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LAdump - Online in the Cloud

Run LAdump in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command LAdump that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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.

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