gatk-3.8/public
David Roazen 884d031e72 NestedIntegerArray: Pre-allocate only the first two dimensions
It turns out that pre-allocating the entire tree was too expensive in
terms of memory when using large values for the -mcs and -ics parameters.

Pre-allocating the first two dimensions prevents us from ever locking the
root node during a put(). Contention between threads over lower levels
of the tree should be minimal given that puts are rare compared to gets.

Also output dimensions and pre-allocation info at startup. If pre-allocation
takes longer than usual this gives the user a sense of what is causing the
delay.
2012-10-25 15:17:42 -04:00
..
R Fix a nasty bug in reading GATK reports with a single line 2012-09-10 20:14:13 -04:00
c
chainFiles
doc
java NestedIntegerArray: Pre-allocate only the first two dimensions 2012-10-25 15:17:42 -04:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release. 2012-07-23 16:32:31 -04:00
perl Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters) 2012-06-07 16:56:32 -04:00
scala Better error message when generic types are erased from scala collections. 2012-10-22 16:27:31 -04:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00