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That's why I saved $0 in K: awk 'NR==FNR { K[$1,$2,$3]=$0; next } ($1,$2,$3) in K { print $0, K[$1,$2,$3] }' a b

Just for your info,

($1 SUBSEP $2 SUBSEP $3) and

($1, $2, $3)are equivalent.

So you could use:
($1, $2, $3) in K

You can use the NR==FNR trick to avoid needing your own read-loop for the first file. FNR is the line number in the file, NR is the total number of lines; they are only the same when you're reading...

Alister's solution sure simpliest and better but if you want to do it with awk then using different seperator rather than "A" cold be better i guess:
echo...

Try this one liner awk, see if it helps:

echo "m110730_101608_00120_c100168052554400000315046108261127_s1_p0/7/29_426ACGTGCTATGCGG"|awk -F'A' '{print $1 " " "A" $2 $3}'

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You can't expect characters that are used to split a string to be part of the result. If you split "1,2,3,4" on the comma, by definition the comma is not an allowed member of a field. Same goes...

Not tested:
printf( "%s\t%s\n", k2rec[key,i], $0) > k2rec[key,i]

The short answer is to process f2 first, then process f1. This will reduce your memory footprint as you'll only save 68 things in a[] rather than 48K things.

The long answer is to be a bit more...

<42MLN.3.bedS2 xargs -i grep {} testRef2or
<42MLN.3.bedS2 xargs -I{} grep {} testRef2# cat f3
13208
13208
13360
13363
13484
13518
13518
# cat f2
A1BG - 13208 13284
AAA1 - ...

awk 'NR==FNR{a[NR]=$1;s=NR;next}
{for (i=1;i<=s;i++) if (a[i]>=$3&&a[i]<=$4) {print a[i] "\t" $0}}' 42MLN.3.bedS2 testRef2

13208 A1BG - 13208 13284
13208 A1BG - 13208 ...