Hello
I have a file containing a list of aligned Refseq identifier in the
following format.  I want to convert this file into RangedData format in
such a way that  "findOverlaps" function be as efficient as possible. I know
how to do this when each of the identifiers has just a start and an end
coordinate. IRanges package is very efficient in finding the overlapping
intervals in such case. But when the structure is in the form of blobs (as
shown below in the last three fields), I am not sure how to convert this
structure into RangedData format and how to subsequently call the
"findOverlaps" function.

RefSeqID               targetName    strand        blockSizes
queryStart             targetStart
XM_001065892.1    chr4                 +            127,986,
0,127,                  124513961,124514706,
XM_578205.2         chr2                  -             535,137,148,
   0,535,672,            155875533,155879894,155895543,
NM_012543.2         chr1                 +             506,411,212,494,
0,506,917,1129,    96173572,96174920,96176574,96177991,

Thanks and appreciate ur help.
--Fahim

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