zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/public/java/src/org/broadinstitute/sting/utils
History
Eric Banks 66c652d687 Added some extra error checks in the VCF codec. Now that we've moved this back into the GATK, changed some of the standard exceptions to be USerErrors (instead of TribbleExceptions). 2011-07-14 11:56:10 -04:00
..
analysis Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
baq Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
bed Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
classloader Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
clipreads Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
codecs Added some extra error checks in the VCF codec. Now that we've moved this back into the GATK, changed some of the standard exceptions to be USerErrors (instead of TribbleExceptions). 2011-07-14 11:56:10 -04:00
collections Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
duplicates Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
exceptions Added some extra error checks in the VCF codec. Now that we've moved this back into the GATK, changed some of the standard exceptions to be USerErrors (instead of TribbleExceptions). 2011-07-14 11:56:10 -04:00
fasta Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache 2011-07-01 16:04:30 -04:00
file Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
genotype Bug fix: if we're genotyping a very long indel (>100 bp) fail gracefully instead of with an array out of bounds exception 2011-07-08 12:48:49 -04:00
help Modified build.xml and the help extractor doclet to use the output of "git 2011-06-28 08:37:05 -04:00
instrumentation Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
interval Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
pileup Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
sam Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
text Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
threading Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
variantcontext Allowing VCF records without GTs in vf4.1 2011-07-13 09:56:08 -04:00
wiggle Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
yaml Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
BaseUtils.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
DisjointSet.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLoc.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocParser.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocSortedSet.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
HasGenomeLocation.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
HeapSizeMonitor.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
IndelUtils.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MannWhitneyU.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MathUtils.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MendelianViolation.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PathUtils.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
QualityUtils.java This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation. 2011-07-12 14:11:53 -04:00
ReservoirDownsampler.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
SWPairwiseAlignment.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
SampleUtils.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
SequenceDictionaryUtils.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
SimpleTimer.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
Utils.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00