A frg file created by TracearchiveToCA contains an entry with these values:
which would seem to be allowed by the description here:
1. To indicate that either the vector or quality clear range is not known, omit the clv: or clq: entry. 2. To indicate no sequence is in a clear range, any begin >= end may be used, with 0,0 being the standard. For example, "clr:0,0".
(caveat, there is a warning that isn't up to to date, but I could not find the source for what was.) Unfortunately the 0,-1 pair is toxic to the gatekeeper built from trunk on 2014_07_03 because AS_PER_gkStore_clearRange.C contains:
assert(begin <= end);
assert(begin <= fr->gkFragment_getSequenceLength());
assert(end <= fr->gkFragment_getSequenceLength());
end is unfortunately passed as a uint32, so -1 turns into 2^32-1 which is longer than the sequencelength, and gatekeeper aborts.
Either TracearchiveToCA needs to use something other than 0,-1 or gatekeeper needs to handle that end as a signed value. Or both.
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