I have a file named snp_data containing 5 million SNPs. This is a 3-column, white-space delimited CSV file which has the following format:

snp_id    chromosome  position
Chr01__912 1 912 
Chr01__944 1 944 
Chr01__1107 1 1107 
Chr01__1118 1 1118 
Chr01__1146 1 1146 
Chr01__1160 1 1160 
...
...
...
Chr10__214708367 10 214708367
Chr10__214708424 10 214708424
Chr10__214708451 10 214708451
Chr10__214708484 10 214708484
Chr10__214708508 10 214708508

Note that for each row the snp_id field has the form Chr{chromosome}__{position} for the corresponding values of chromosome and position.

I have another file named window containing auxiliary data. This is a 5-column, white-space delimited CSV file which has the following format:

cat window

seqname chromosome start end width
1 Chr1 1 15000 15000
2 Chr1 15001 30000 15000 
3 Chr1 30001 45000 15000
4 Chr1 45001 60000 15000 
5 Chr1 60001 75000 15000 
6 Chr1 75001 90000 15000 
...
...
...
199954 Chr10 214620001 214635000 15000
199955 Chr10 214635001 214650000 15000
199956 Chr10 214650001 214665000 15000
199957 Chr10 214665001 214680000 15000
199958 Chr10 214680001 214695000 15000
199959 Chr10 214695001 214708580 13580

Note the correspondence between the window and snp_data files determined by the value of the chromosome field in the window file and the values of the chromosome and snp_id fields in the snp_data file, e.g. rows with a value of "Chr1" in window correspond to rows in snp_data with a value of 1 for chromosome and whose snp_id rows begin with a prefix of Chr01__.

For each row in the snp_data file (each snp within each chromosome), if that row's position value falls within the range given by the start and end values of any of the rows in window for that particular chromosome, then append the seqname from the window file to the row from the snp_data file.

For the input given above, this would be my desired output: