xenial (1) LAdump.1.gz

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)