I don't understand your sample. Your "another file" is described two ways:

Code:

(with header, multiple rows and cols, each sample has 3 values a,b,c)

and

Code:

(no header first 3 cols)

and I don't see any way to turn:

Code:

sample2 B
sample3 B
sample6 D
sample7 D

into:

Code:

sample2 sample3 sample6 sample7
chr start end a2 b2 c2 a3 b3 c3 a6 b6 c6 a7 b7 c7 
chr start end ....

nor why you describe this as:

Code:

(no header first 3 cols)

when the 1st line sort of looks like a header and the 2nd line has 15 columns.

The .... doesn't appear to be a literal string, but I can't figure out what additional data you want if the .... is intended to be an ellipsis indicating that more data is to follow.

Please try again to clearly explain how the input files are to be transformed into the output you want.