Re^8: What is the best approach to check if a position falls within a target range?

Hi BrowserUk,
The target region is a chromosome bed file which spans on an average a 300 base region on any chromosome. Let us say the target region contains incremental regions of 300 each. I am trying to identify if a SNP falls in the target region. 2**16 or 2**32 as max is really too big!

target region
=============
chr1 100 400
chr1 450 750
chr1 780 980
...
[download]

Thanks Much,
Uma

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Re^9: What is the best approach to check if a position falls within a target range? by BrowserUk (Patriarch) on Feb 12, 2011 at 15:25 UTC
Hm. A file containing 2 million queries consisting of a single integer in the range 1 .. 1000, is going to contain (on average) 1000 duplicates of each query? Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice.	[reply]
Re^10: What is the best approach to check if a position falls within a target range? by umasuresh (Hermit) on Feb 12, 2011 at 15:50 UTC
Hi BrowserUk, I am sorry I don't understand your question! I am trying to output something like this: `Query ===== 89 100 200 416 500 780 Target ====== 100_400 420_720 800_1100 Output ======= 89 not_in_target 100 100_400 200 100_400 416 not_in_target 500 420_720 780 not_in_target` [download]	[reply] [d/l]
Re^11: What is the best approach to check if a position falls within a target range? by BrowserUk (Patriarch) on Feb 12, 2011 at 16:20 UTC
I am sorry I don't understand your question! You said that the query file contains 2 million queries. You said that the maximum number is much less than 2**16, and your in your sample data all the numbers are less than 1000. If all the numbers are less than 1000 and you have 2 million of them, then on average, each query will be duplicated 2000 times. Which suggests that if you pre-processed your queries file to remove the duplication, you would end up with 1000 queries only and so would reduce the amount of work to do by 3 orders of magnitude. Ie. Your processing would be 2000 times faster. All of which suggests either your queries are more than just a single integer, or the range is much larger. Which is it? Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice.	[reply]