08-08-2012
Oh ok. I think what I need the difference between two columns. To provide some context the A's and G's are biological genetic mutation data. One column is the reference, and the other is a tumor sample. I am trying to extract all entries where there is an insertion OR deletion of at least 3base pairs (A's G's C's or T's).
The best way to do this is to look at the reference and tumor column and ask if there is at least a difference of 3 letters.
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IGAWK(1) Utility Commands IGAWK(1)
NAME
igawk - gawk with include files
SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ...
igawk [ all gawk options ] [ -- ] program-text file ...
DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1).
AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like
@include getopt.awk
in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path.
OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports.
EXAMPLES
cat << EOF > test.awk
@include getopt.awk
BEGIN {
while (getopt(ARGC, ARGV, "am:q") != -1)
...
}
EOF
igawk -f test.awk
SEE ALSO
gawk(1)
Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995.
AUTHOR
Arnold Robbins (arnold@skeeve.com).
Free Software Foundation Nov 3 1999 IGAWK(1)