awk to find overlaps -

i have file columns shown below.

group   start        end chr1    117132092    118875009 chr1    117027758    119458215 chr1    103756473    104864582 chr1    105093795    106219211 chr1    103354114    104747251 chr1    102741437    105235140 chr1    100090254    101094139 chr1    100426977    101614730 chr2    86644663     87767193 chr2    82473711     83636545 chr2    83896702     85079032 chr2    83876122     85091910 chr2    82943211     84350917 chr3    89410051     90485635 chr3    89405753     90485635 chr3    86491492     87593215 chr3    82507157     83738004 chr3    85059618     86362254 

i find overlap between coordinates in each group(grouped chr1,chr2,chr3..).

the start , end coordinates has checked if there atleast 50% overlap others in same group. if there atleast 50% overlap, new start , end coordinates has reported in columns 3 , 4 (which range of overlap region). if don't overlap has report original start , end in columns 3 , 4.

to make more clear, lets take first 2 rows

                 117132092..........118875009          117027758...........................119458215 

since both of them overlap atleast 50% each other, range of overlap reported new start , new end in output. , row 3 , 4 doesn't overlap others , original coordinates reported new start , new end in column 3 , 4. , again since rows 5 , 6 have 50% overlap each other range reported new start , new end in column 3 , 4. here expected output:

group   start     end         newstart   newend    chr1 117132092 118875009  117027758   119458215 chr1 117027758 119458215  117027758   119458215 chr1 103756473 104864582  103354114   104864582 chr1 105093795 106219211  105093795   106219211 chr1 103354114 104747251  102741437   105235140 chr1 102741437 105235140  102741437   105235140 chr1 100090254 101094139  100090254   101614730 chr1 100426977 101614730  100090254   101614730 chr2 86644663 87767193    86644663    87767193 chr2 82473711 83636545    82473711    83636545  chr2 83896702 85079032    83876122    85091910 chr2 83876122 85091910    83876122    85091910 chr2 82943211 84350917    82943211    84350917 chr3 89410051 90485635    89405753    90485635 chr3 89405753 90485635    89405753    90485635 chr3 86491492 87593215    86491492    87593215 chr3 82507157 83738004    82507157    83738004 chr3 85059618 86362254    85059618    86362254 

i have achieved in r programming language original file huge , take long time run. in awk.

using gnu awk version 4, try:

gawk -f a.awk file file 

where a.awk is:

nr==fnr {     if (fnr>1) {         a[$1][++i]=$2         b[$1][i]=$3     }     next } fnr==1 {     fmt="%-7s%-10s%-10s%-10s%-10s\n"     printf fmt,"group","start","end","newstart","newend"  } fnr>1{     $4=$2; $5=$3     n=checkinside($1,$2,$3)     if (n>0) {         ff=0; x=$2; y=$3         (i=1; i<=n; i++) {             ar=a[$1][r[i]]; br=b[$1][r[i]];             getintersect($2,$3,ar,br)             getlargest($2,$3,ar,br)             ovl=((i2-i1)/($3-$2))*100;             ovr=((i2-i1)/(br-ar))*100;             if (ovl>50 && ovr>50) {                 if (r1<x) x=r1                 if (r2>y) y=r2                 ff=1             }         }         if (ff) {             $4=x; $5=y         }     }     printf fmt,$1,$2,$3,$4,$5 }  function getlargest(x1,y1,x2,y2) {     r1=(x1<=x2)?x1:x2     r2=(y1>=y2)?y1:y2 }  function getintersect(x1,y1,x2,y2) {     if (x1>=x2 && x1<=y2) {         i1=x1;     } else {         i1=x2;     }     i2=(y1<=y2)?y1:y2 }  function checkinside(g,x,y,i,j,x1,y1) {     r["x"]=0     (i in a[g]) {         x1=a[g][i]; y1=b[g][i];         if ((x>=x1 && x<=y1) || (y>=x1 && y<=y1)) {             if (!(x==x1 && y==y1))                 r[++j]=i         }     }     return j } 

output:

group  start     end       newstart  newend     chr1   117132092 118875009 117027758 119458215  chr1   117027758 119458215 117027758 119458215  chr1   103756473 104864582 103354114 104864582  chr1   105093795 106219211 105093795 106219211  chr1   103354114 104747251 102741437 105235140  chr1   102741437 105235140 102741437 105235140  chr1   100090254 101094139 100090254 101614730  chr1   100426977 101614730 100090254 101614730  chr2   86644663  87767193  86644663  87767193   chr2   82473711  83636545  82473711  83636545   chr2   83896702  85079032  83876122  85091910   chr2   83876122  85091910  83876122  85091910   chr2   82943211  84350917  82943211  84350917   chr3   89410051  90485635  89405753  90485635   chr3   89405753  90485635  89405753  90485635   chr3   86491492  87593215  86491492  87593215   chr3   82507157  83738004  82507157  83738004   chr3   85059618  86362254  85059618  86362254