Re^2: How to make a hash to evaluate columns between large datasets

Here is a head from my input file, and the columns are the following information: ID, strand, chromosome, start, sequence, quality score, and positions in the genome. The last two are unnecessary for what I need, so the script is only defining strand, chromosome, start, and length of sequence to find the end. I use these to then parse through the reference file to grab the info in the last column of the reference, and append most of the info from the original input.

I chose this header as it has some of info I hope to overlook, such as chromosome missing in the reference (line 1) and different sites on the same chromosome (lines 3 and 4).

3-51568    +    HSV1_17    9285    TGGGCAAACACTTGGGGACTG    IIIIIIIIII
+IIIIIIIIIII    0
2-70337    +    KI270733.1    135235    TCGCTGCGATCTATTGAAAGTCAGCCCTCG
+ACACAAGGGTTTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    4  
+  
2-70337    +    21    8446166    TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAG
+GGTTTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    4    
2-70337    +    21    8218896    TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAG
+GGTTTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    4    
2-70337    +    GL000220.1    118372    TCGCTGCGATCTATTGAAAGTCAGCCCTCG
+ACACAAGGGTTTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    4  
+  
2-70337    +    21    8401935    TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAG
+GGTTTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    4    
1-130983    +    2    32916254    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    IIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    5    
1-130983    +    2    32916255    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    IIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    5    
1-130983    +    2    32916256    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    IIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    5    
1-130983    +    2    32916257    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    IIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    5
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