gatk-3.8/public
Eric Banks a26b04ba17 Extensive refactoring of the GATKReports. This was a beast.
The practical differences between version 1.0 and this one (v1.1) are:

* the underlying data structure now uses arrays instead of hashes, which should drastically reduce the memory overhead required to create large tables.
* no more primary keys; you can still create arbitrary IDs to index into rows, but there is no special cased primary key column in the table.
* no more dangerous/ugly table operations supported except to increment a cell's value (if an int) or to concatenate 2 tables.

Integration tests change because table headers are different.
Old classes are still lying around.  Will clean those up in a subsequent commit.
2012-05-18 01:11:26 -04:00
..
R Add warning message about ratios in variantQCreport, give ratio for MAF > 10% 2012-04-25 12:22:32 -04:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
doc Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
java Extensive refactoring of the GATKReports. This was a beast. 2012-05-18 01:11:26 -04:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages build system overhaul 2012-05-17 15:16:29 -04:00
perl Update to the bindings for liftOverVCF.pl (to -V from -B) 2011-09-15 15:33:09 -04:00
scala Extensive refactoring of the GATKReports. This was a beast. 2012-05-18 01:11:26 -04:00
testdata Extensive refactoring of the GATKReports. This was a beast. 2012-05-18 01:11:26 -04:00