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Full Discussion: Building intervals
Top Forums UNIX for Dummies Questions & Answers Building intervals Post 302904432 by SriniShoo on Wednesday 4th of June 2014 05:50:02 AM
Old 06-04-2014
looks like the below line from the expect output is incorrect
Code:
chr1   153234602   155205669   GBA   1971067

it should be
Code:
chr1 155205331 155205669 GBA 338

If my assumption is true, below code should do
Code:
awk 'NR == 1 {print; next}
{ if (t == ($1 FS $5) && $4 == "hom") {FLG++}
  else if ($4 == "hom"){t = ($1 FS $5); START = $2; FLG = 0}
  else {t = ""; FLG = 0}
  if (FLG == 1) {STR[++n] = START; CHR[n] = $1; STP[n] = $3; GEN[n] = $5}
  else if (FLG > 1) {STP[n] = $3}}
END {for(i = 1; i <= n; i++)
  {print CHR[i], STR[i], STP[i], GEN[i], (STP[i] - STR[i])}}' file

This User Gave Thanks to SriniShoo For This Post:
 

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PAPS(1) 						      General Commands Manual							   PAPS(1)

NAME
paps - UTF-8 to PostScript converter using Pango SYNOPSIS
paps [options] files... DESCRIPTION
paps reads a UTF-8 encoded file and generates a PostScript language rendering of the file. The rendering is done by creating outline curves through the pango ft2 backend. OPTIONS
These programs follow the usual GNU command line syntax, with long options starting with two dashes (`-'). A summary of options is included below. --landscape Landscape output. Default is portrait. --columns=cl Number of columns output. Default is 1. --font=desc Set the font description. Default is Monospace 12. --rtl Do rtl layout. --paper ps Choose paper size. Known paper sizes are legal, letter, a4. Default is A4. --bottom-margin=bm Set bottom margin in postscript points (1/72 inch). Default is 36. --top-margin=tm Set top margin. Default is 36. --left-margin=lm Set left margin. Default is 36. --right-margin=rm Set right margin. Default is 36. --help Show summary of options. --header Draw page header for each page. --markup Interpret the text as pango markup. --encoding=ENCODING Assume the documentation encoding is ENCODING. --lpi Set the lines per inch. This determines the line spacing. --cpi Set the characters per inch. This is an alternative method of specifying the font size. --stretch-chars Indicates that characters should be stretched in the y-direction to fill up their vertical space. This is similar to the texttops behaviour. AUTHOR
paps was written by Dov Grobgeld <dov.grobgeld@gmail.com>. This manual page was written by Lior Kaplan <kaplan@debian.org>, for the Debian project (but may be used by others). April 17, 2006 PAPS(1)
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