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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
..
vcf Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
HiSeq.10000.bgzip.vcf.gz Adding bgzip vcf file for unit tests 2011-09-21 15:39:45 -04:00
HiSeq.10000.vcf Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
HiSeq.10000.vcf.gz GZIP VCF for testing 2011-08-19 09:05:39 -04:00
TabularDataTest.dat Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
TabularDataTest2.dat Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ValidatingPileupTargets.list Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ac0.vcf VariantEval now includes -keepAC0 argument to include sites with alt alleles but AC 0 in analyses 2012-04-04 15:37:12 -04:00
breakpoint-example.vcf Added support for breakpoint alleles 2012-02-23 12:14:48 -05:00
ceutrio.ped Oops, forgot the PED test file 2011-10-05 21:09:08 -07:00
defaultGATKConfig.cfg Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
diffTestMaster.vcf First working version of the DiffNode readers for VCF and BAM files. Unit tests confirm the readers are approximately working. Skeleton of a working DiffObjects walker that will be able to provide detailed information about how exactly two files of the same type differ, so long as the files are supported by the DiffNode structure. 2011-07-04 16:11:42 -04:00
diffTestTest.vcf First working version of the DiffNode readers for VCF and BAM files. Unit tests confirm the readers are approximately working. Skeleton of a working DiffObjects walker that will be able to provide detailed information about how exactly two files of the same type differ, so long as the files are supported by the DiffNode structure. 2011-07-04 16:11:42 -04:00
exampleBAM.bam PPP pipeline test 2011-12-11 17:32:21 -05:00
exampleBAM.bam.bai PPP pipeline test 2011-12-11 17:32:21 -05:00
exampleBAM.simple.bai Testdata for diffObjects. 2011-07-18 10:47:03 -04:00
exampleBAM.simple.bam Testdata for diffObjects. 2011-07-18 10:47:03 -04:00
exampleDBSNP.vcf PPP pipeline test 2011-12-11 17:32:21 -05:00
exampleFASTA.dict Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
exampleFASTA.fasta Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
exampleFASTA.fasta.amb Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.ann Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.bwt Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.fai Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
exampleFASTA.fasta.pac Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.rbwt Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.rpac Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.rsa Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.sa Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleGRP.grp Extensive refactoring of the GATKReports. This was a beast. 2012-05-18 01:11:26 -04:00
exampleNORG.bam Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
exampleNORG.bam.bai Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
gFFTest.gff Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
gatkrunreport.fail.xml analyzeRunReports cleanup for new minimal GATKRunReport structure 2012-03-12 09:46:26 -04:00
gatkrunreport.success.xml analyzeRunReports cleanup for new minimal GATKRunReport structure 2012-03-12 09:46:26 -04:00
genotypes_chr1_ASW_phase3.3_first500.hapmap Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
logisticParamsTest.list Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
overlapTest.bed Testdata for IntervalStratification 2011-11-10 11:08:34 -05:00
recalConfig_1KG.cfg Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
sampleBedFile.bed Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
small.dbsnp.rod Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
tranches.4.txt Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
tranches.6.txt Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
tranches.raw.dat Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
withSymbolic.b37.vcf Testdata for IntervalStratification 2011-11-10 11:08:34 -05:00