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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Mark DePristo 233f70f8ba Final cleanup of TraversalProgressMeters, moved to utils.progressmeter 
-- TraversalProgressMeter now completely generalized, named ProgressMeter in utils.progressmeter.  Now just takes "nRecordsProcessed" as an argument to print reads.  Completely removes dependence on complex data structures from TraversalProgressMeter.  Can be used to measure progress on any task with processing units in genomic locations.
-- a fairly simple, class with no dependency on GATK engine or other features.
-- Currently only used by the TraversalEngine / MicroScheduler but could be used for any purpose now, really.
 		2012-09-10 20:14:14 -04:00
..
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 - New UserExceptions added for when ReadFilters or Walkers specified on the command line are not found. When -rf xxxx cannot find the class corresponding to xxxx, all read filters are printed in a better formatted way, with links to their gatk docs. 2012-09-04 16:41:44 -04:00
clipping fixing typo 2012-09-05 10:41:03 -04:00
codecs Print "Parsing data stream with BCF version BCFx.y" in BCF2 codec as .debug not .info 2012-08-19 10:32:55 -04:00
collections Refactored/renamed the nested integer array; cleaned up code a bit. 2012-07-03 00:12:33 -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 Extensions to the ErrorThrowing framework for testing purposes 2012-09-06 22:03:18 -04:00
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
help Added forum API version stub to base URL for posting GATKDocs 2012-09-07 11:49:02 -04:00
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 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
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 Final cleanup of TraversalProgressMeters, moved to utils.progressmeter 2012-09-10 20:14:14 -04:00
recalibration 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
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 Refactor TraversalEngine to extract the progress meter functions 2012-09-10 20:14:13 -04:00
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 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
variantcontext After dicussion with Ryan/Eric, the Structural_Indel variant type is now gone, and has been entirely replaced with the access pattern .isStructuralIndel(). This makes it a strict subtype of indel. I agree that this method is a bit more sensible. 2012-08-30 17:57:31 -04:00
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 Clean, documented implementation of ThreadFactory that monitors running / blocking / waiting time of threads it creates 2012-08-15 21:13:15 -04:00
BaseUtils.java Just noticed that the efficient conversion to uppercase method is redundant since it's already implemented efficiently in Picard; let's just have a single implementation. 2012-08-22 11:26:08 -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 Removing parallelism bottleneck in the GATK 2012-08-15 21:13:15 -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 Another round of FindBugs fixes. Object returns its internal reference to an externally mutable array. Very dangerous. 2012-08-21 09:35:55 -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 Another round of FindBugs fixes. Comparator doesn't implement Serializable. 2012-08-21 09:20:55 -04:00
MathUtils.java Downsampling: experimental engine integration 2012-09-06 15:03:27 -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
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
PairHMM.java A few quick, minor findbugs fixes. 2012-08-09 16:30:58 -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 Done GSA-539: SimpleTimer should use System.nanoTime for nanoSecond resolution 2012-09-05 15:45:23 -04:00
Utils.java Working (efficient?) implementation of NanoScheduler 2012-08-24 15:34:23 -04:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00