The bin field is extremely useful for indexing purposes. I have found the appropriate documentation and code for bit-shifting bin calculations. I have two questions regarding bin implementation.
[1] Are the bin calculations in the UCSC genome-browser based on the standard 0-based UCSC start position, half-open? Or are they calculated based on 1-based fields, inclusive? I am using this field to intersect with a custom field that uses bin and therefore the difference is important. The code subtracting 1 from the end position makes me think the coordinates are half-open, but I am still unsure of 0-base versus 1-base. [2] How is the calculation of which bins to search determined at query time for the UCSC genome browser, i.e. is there a join of bin to a bin table (or a subquery), is there an SQL function / stored proc to return possible bins, or is something done at the level of AJAX/PHP to decide which bins to look in for overlapping features? Thanks for the clarifications. Eli Roberson _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
