original positions in reads

major major at genome.wi.mit.edu
Thu Jul 19 12:12:25 EST 2001


Hello,
I'd like to get the original position info directly from the gapDB
instead of from the dumped out experiment files(where the info is tagged
"ON   1..70 0 71..87 0 88..657 659..763"). I want to compare the source
info with the edits that have been made while creating the gapDB.  I can
access the positional info for each read, but get this type of array
returned:
_____________________--
2 5 2 4 2 3 2 2 2 1 2 0 1 -1 1 -2 1 -3 1 -4 1 -5 1 -6 1 -7 1 -8 1 -9 1
-10 1 -11 1 -12 1 -13 1 -14 1 -15 1 -16 1 -17 1 -18 1 -19 1 -20 1 -21 1
-22 1 -23 1 -24 1 -25 1 -26 1 -27 1 -28 1 -29 1 -30 1 -31 1 -32 1 -33 1
-34 1 -35 1 -36 1 -37 1 -38 1 -39 1 -40 1 -41 1 -42 1 -43 1 -44 1 -45 1

How do I resolve from this array where the insertions and deletions were
made?

Thanks-
John Major

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