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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Eric Banks e199562c25 I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever). 2012-11-27 10:26:17 -05:00
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R Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller. 2012-04-17 14:22:48 -04:00
activeregion Merged bug fix from Stable into Unstable 2012-08-22 14:40:34 -04:00
analysis Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
baq Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)" 2012-09-10 15:52:39 -04:00
classloader Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component. 2012-10-16 02:22:30 -04:00
clipping fixing typo 2012-09-05 10:41:03 -04:00
codecs Bugfix for GSA-540 / Update metadata maps when adding lines to VCFHeader 2012-10-26 16:34:16 -04:00
collections NestedIntegerArray: Pre-allocate only the first two dimensions 2012-10-25 15:17:42 -04:00
crypt Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
duplicates GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
exceptions I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever). 2012-11-27 10:26:17 -05:00
fasta Ensure thread-safety of CachingIndexedFastaSequenceFile 2012-08-27 12:11:54 -04:00
file Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
fragments Fixing bug from when FragmentUtils merging function moved over to the soft clipped start instead of the unclipped start 2012-08-30 10:10:43 -04:00
genotyper Added allele biased down-sampling capabilities to the PerReadAlleleLikelihoodMap object, which means that both the UG and HC can use this functionality. Note that it's only available in protected, so GATK-lite users won't be allowed to enable it. Needs more testing. 2012-10-24 22:52:25 -04:00
help I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever). 2012-11-27 10:26:17 -05:00
instrumentation Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
interval Quick pass of FindBugs 'inefficient use of keySet iterator instead of entrySet iterator' fixes for core tools. 2012-08-08 14:29:41 -04:00
io One less Queue command line requirement: -tempDir now defaults to .queue/tmp. 2012-08-27 12:04:50 -04:00
nanoScheduler Fix thread name: should be master executor not input 2012-09-24 14:15:35 -04:00
pairhmm Refactoring the PairHMM util class to allow for multiple implementations which can be specified by the callers via an enum argument. Adding an optimized PairHMM implementation which caches per-read calculations as well as a logless implementation which drastically reduces the runtime of the HMM while also increasing the precision of the result. In the HaplotypeCaller we now lexicographically sort the haplotypes to take maximal benefit of the haplotype offset optimization which only recalculates the HMM matrices after the first differing base in the haplotype. Many thanks to Mauricio for all the initial groundwork for these optimizations. The change to the one HC integration test is in the fourth decimal of HaplotypeScore. 2012-10-20 16:38:18 -04:00
pileup Downsampling: experimental engine integration 2012-09-06 15:03:27 -04:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
progressmeter Add GATK-wide command line argument to control the maximum runtime allowed for the GATK 2012-10-26 13:18:34 -04:00
recalibration Fixed nasty bug in BQSR csv file creation: 2012-11-09 08:33:55 -05:00
runtime No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. 2011-10-27 14:17:07 -04:00
sam Apparently CIGAR elements can have 0 length according to the spec, but 0Ms were causing left alignment of indels to fail. Fixed. 2012-11-06 20:53:33 -08:00
text Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller. 2012-04-17 14:22:48 -04:00
threading BQSR: use more granular locking for concurrency control 2012-10-24 15:22:50 -04:00
variantcontext I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever). 2012-11-27 10:26:17 -05:00
wiggle Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
AminoAcid.java Removing the Genomic Annotator and its supporting classes 2011-07-25 15:10:25 -04:00
AminoAcidTable.java Removing the Genomic Annotator and its supporting classes 2011-07-25 15:10:25 -04:00
AutoFormattingTime.java Add GATK-wide command line argument to control the maximum runtime allowed for the GATK 2012-10-26 13:18:34 -04:00
BaseUtils.java Protect against bad bases users have screwy data (or try to use zipped references) 2012-10-12 15:05:03 -04:00
BitSetUtils.java Refactoring of BQSRv2 to use longs (and standard bit fiddling techniques) instead of Java BitSets for performance improvements. 2012-06-12 09:19:36 -04:00
ContigComparator.java Documented following the new gatkdoc framework 2011-07-25 00:25:08 -04:00
GenomeLoc.java Bugfix to compareTo and equals in GenomeLoc 2012-08-30 19:41:49 -04:00
GenomeLocComparator.java Optimized interval iteration 2011-09-28 16:07:34 -04:00
GenomeLocParser.java Fixes GSA-515 Nanoscheduler GSA-577 -nt and -nct together appear to not close resources properly 2012-09-24 14:15:35 -04:00
GenomeLocSortedSet.java Active region walkers can now see the reads in a buffer around thier active reigons. This buffer size is specified as a walker annotation. Intervals are internally extended by this buffer size so that the extra reads make their way through the traversal engine but the walker author only needs to see the original interval. Also, several corner case bug fixes in active region traversal. 2012-01-19 22:05:08 -05:00
Haplotype.java Refactoring the PairHMM util class to allow for multiple implementations which can be specified by the callers via an enum argument. Adding an optimized PairHMM implementation which caches per-read calculations as well as a logless implementation which drastically reduces the runtime of the HMM while also increasing the precision of the result. In the HaplotypeCaller we now lexicographically sort the haplotypes to take maximal benefit of the haplotype offset optimization which only recalculates the HMM matrices after the first differing base in the haplotype. Many thanks to Mauricio for all the initial groundwork for these optimizations. The change to the one HC integration test is in the fourth decimal of HaplotypeScore. 2012-10-20 16:38:18 -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 Improvements to indel analysis capabilities of VariantEval 2012-04-06 16:07:46 -04:00
MannWhitneyU.java A couple of minor things. 2012-09-20 12:48:13 -04:00
MathUtils.java Merge AFCalcResultTracker into StateTracker, cleanup 2012-10-21 12:42:31 -04:00
Median.java ReadGroupProperties walker and associated infrastructure 2012-03-01 15:01:11 -05:00
MendelianViolation.java Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
MultiThreadedErrorTracker.java Proper error handling in NanoScheduler 2012-09-19 17:03:13 -04:00
NGSPlatform.java Stabilized NGSPlatform code: don't assume all reads have read groups (e.g. artificial SAM records) 2012-06-06 15:17:30 -04:00
PathUtils.java GATKPerformanceOverTime script update 2012-01-02 09:58:46 -05:00
QualityUtils.java Extensive unit tests, contacts, and documentation for RecalDatum 2012-07-31 08:11:03 -04:00
ReservoirDownsampler.java Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
SWPairwiseAlignment.java FindBugs 'Efficiency' fixes 2012-08-16 15:40:52 -04:00
SampleUtils.java Phase I commit to get shadowBCFs passing tests 2012-06-21 15:16:26 -04:00
SequenceDictionaryUtils.java Quick pass of FindBugs 'method invokes inefficient Number constructor' fixes. 2012-08-08 14:34:16 -04:00
SimpleTimer.java Fixes GSA-515 Nanoscheduler GSA-560 / Fix display of NanoScheduler and MonitoringEfficiency 2012-09-11 07:38:34 -04:00
Utils.java Framework for evaluating the performance and scaling of the ExactAF models 2012-10-03 19:55:11 -07:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00