01-19-2019
Quote:
Are the ranges given in your first input file always in increasing numerical order for each $1,$4 set of values (as in your sample file f1)? If they are we can use that information to make your code run faster.
Yes, these should always be sorted like in
f1
Quote:
Is the fifth subfield of $4 in your second input file always identical to the $1 value on the same input line (as in your sample files)? If they are, we can use that information to make your code run faster.
Yes, this will always be the case if
$4 is found as in
f1
Quote:
You note that your input files fields are separated by tabs. Do you want the output file to be tab delimited too; or do you want the output to be delimited by spaces as shown in your sample output?
f1 will always be
tab-delimited except for a whitespace after
$3 and
$4, but the output would be
tab-delimited I did and
OFS="\t" but I think the whitespaces are making that not work
You are correct in that I meant to be looking for inclusive endpoints so the
>=/<= is what I should have used.
Quote:
Is it your intent to print the line containing exon if either endpoint is in an entry in the first input file for that $1,$4 pair, or should it only print the exon line if both endpoints are in range?
I used the
|| statement to make sure the script works as expected but it could be
&& as both coordinates should lie within the endpoints (trying to think of a situation where its not the case and not coming up with anything).
Thank you very much
.
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