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The gsub statement is just replacing and counting single letters, so it does not look at fields and whether the pattern is the entire field...

Try a loop instead:
awk 'BEGIN{print "count"}...

Slight simplification:awk '
{printf "%s\t%s\t%s\t", $1, $2, $3
for (i=4; i<=NF; i+=2) {if ($i==$(i+1) || $(i+1) == "NN") printf "%s\t", $i
else ...

Hi, here a corrected version of your script:
awk '{
printf("%s\t%s\t%s\t",$1,$2,$3)
for(i=4;i<=NF;i+=2){
if($i==$(i+1)) new=$i;
else if($i=="NN" || $(i+1)!="NN") new=$(i+1);
else...

Try:
tr -s '\t' < file



--
Note: RavinferSing13's suggestion works also, as long as there are no spaces somewhere in the input file, only TABS

Hello huiyee1,

Could you please try following, it may help you.

awk '{$1=$1} 1' OFS="\t" Input_file


Output will be as follows.

LG10_PM_map_19_LEnd 1000560 G AG AG...

IMHO, awk seems to be the candidate for this job. Use awk to read the title and the next line (using getline function). If the 2nd line (fetched using getline) doesn't start with N, print title and...

sed -n "/^@M/{N;p;}" file

Or

awk ' /^@M/ { getline a; print $0 "\n" a } ' file

awk 'NR%3' file

sed 'n;n;d' file

GNU sed:
sed 0~3d file

Hello All,

Following may help too.



awk '{for(i=1;i<=NF;i++) {if(i%2!=0) {a=a" "$i":"$(i+1)} else{if(i==NF) {print a;a=""} }}}' file_name



Output will be as follows.


1:0...

You can try something like:
awk '{for(i=1;i<=NF;i+=2)printf $i ":" $(i+1) FS}{print ""}' file

What doesn't work? It works with the sample you provided:
sed 's/\([0-9]\) \([0-9]\)/\1:\2/g' file
1:0 0:1 1:1
0:1 1:1 0:0
1:1 0:0 1:1
1:0 0:1 0:1
0:1 0:0 1:0
1:1 1:1 1:1
0:0 0:0 0:0

...