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
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CNV	Nope, loads of integration tests had to be changed.	2012-05-07 14:30:42 -04:00
annotator	Nope, loads of integration tests had to be changed.	2012-05-07 14:30:42 -04:00
beagle	Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .)	2012-01-23 08:25:34 -05:00
bqsr	Extensive refactoring of the GATKReports. This was a beast.	2012-05-18 01:11:26 -04:00
coverage	DoC now properly handles reference N bases + misc. additional cleanups	2012-02-25 11:32:50 -05:00
diagnostics	Extensive refactoring of the GATKReports. This was a beast.	2012-05-18 01:11:26 -04:00
diffengine	Fixing MD5's (new GATKReport header was missing from old md5's)	2012-03-19 15:28:45 -04:00
fasta	Removing the legacy -L "interval1;interval2" syntax	2011-11-21 13:18:53 -05:00
filters	Again, fixing the add call when we really mean replace	2011-11-21 19:15:56 -05:00
genotyper	a) Fully functional and working multiallelic exact model for pools. Needs cleanup/more testing. b) Better unit test for pool genotype likelihoods - it now optionally generates actual noisy pileups that can be used for assessing GL accuracy, c) Totally experimental, hidden option in VariantsToTable to output genotype fields. Specifying -GF will output columns of form Sample.FieldName - needs also more testing	2012-05-14 10:55:35 -04:00
indels	Revving Picard to pick up new SamFileHeaderMerger.	2012-05-02 16:47:28 -04:00
phasing	- Added option to output the father's allele first in phased child haplotypes - BUG corrected causing wrong phasing of child/father pairs	2012-05-03 10:36:49 -04:00
qc	First version of VariantContextBuilder	2011-11-18 11:06:15 -05:00
recalibration	Patching special case in the adaptor clipping	2012-01-11 17:47:44 -05:00
validation	Nope, loads of integration tests had to be changed.	2012-05-07 14:30:42 -04:00
varianteval	Extensive refactoring of the GATKReports. This was a beast.	2012-05-18 01:11:26 -04:00
variantrecalibration	Nope, loads of integration tests had to be changed.	2012-05-07 14:30:42 -04:00
variantutils	Nope, loads of integration tests had to be changed.	2012-05-07 14:30:42 -04:00
BAQIntegrationTest.java	merge master	2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java	Updating MD5s for updated BAM with read groups	2011-10-06 12:15:48 -07:00
FlagStatIntegrationTest.java	Adding integration test for Flag Stat	2012-04-10 22:40:38 -04:00
PileupWalkerIntegrationTest.java	Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.	2012-04-02 14:27:36 -04:00
PrintReadsIntegrationTest.java	Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped	2012-04-27 09:58:38 -04:00
PrintReadsUnitTest.java	Better location for the downsampling of reads in PrintReads	2012-01-14 14:06:09 -05:00