Various updates to have the KB use the expanded exome intervals (from D MacArthur) in addition to chr20.

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1. MergeIntervalLists should take the global interval padding into account when merging.
2. Update the name of the imported callsets in the setup script because of renaming for expanded intervals.
3. If there are too many intervals to process, MongoDB falls apart.  Refactored the site selection code so
   that in such cases we pull out all records from the DB and the GATK itself does the interval filtering.
4. Add isComplex to callset summary for the consensus summarizer.
5. Remove the check for out of order records in the SiteIterator since records now do come out of order
  (since contigs are sorted lexicographically in MongoDB).

Results:
Iteration over the gencode intervals (90 MB) in AssessNA12878 now takes 90 seconds.  I can't tell you how
much time it took before because it kept crashing Mongo (but it was a long, long time).

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This commit is contained in:

Eric Banks 2013-06-17 13:21:21 -04:00

parent ff76d0c877

commit 6dc816beee

Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL

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