#!/usr/bin/env bash
#
###########################################################################
#
# This file is part of Celera Assembler, a software program that
# assembles whole-genome shotgun reads into contigs and scaffolds.
# Copyright (C) 1999-2004, Applera Corporation. All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received (LICENSE.txt) a copy of the GNU General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#
###########################################################################
#
# $Id: breakpoints2StartLenNs.sh,v 1.6 2008/06/27 06:29:16 brianwalenz Exp $
#

awk 'BEGIN{ \
       lastChrom=-1; \
     } \
     { \
       if($2 != lastChrom) \
       { \
         if($1=="N" || $1=="n") \
         { \
           lastN = $3; \
         } \
         else \
         { \
           lastN = -1; \
         } \
         lastChrom = $2; \
       } \
       else \
       { \
         if($1=="N" || $1=="n") \
         { \
           lastN = $3; \
         } \
         else \
         { \
           if(lastN != -1) \
           { \
             print $2, lastN, $3-lastN; \
           } \
           lastN = -1; \
         } \
       } \
     }' ${1} > delme.txt

cat delme.txt ../chrLengths.txt |sort -k 1n -k 2n > chrStartLenNs.txt
