..
analysis
Initial commit of items for analyzing amino acid transitions in variant eval. Blew up my subversion by coding locally while i did not have internet. I hope this doesn't bust any integrationtests since I changed no existing code but...who knows. Crossing my fingers.
2010-06-29 20:57:18 +00:00
baq
-baqGOP now takes phred scaled scores instead of probabilities in the command line.
2011-01-13 00:06:38 +00:00
bed
Convert GenomeLocParser into an instance variable. This change is required
2010-11-10 17:59:50 +00:00
classloader
Stamp out lazy loading in the PluginManager. This is an attempt to stamp
2011-01-13 20:58:28 +00:00
collections
renaming MergingIterator to RODMergingIterator as it is more appropriate for this specialized implementation
2010-10-08 14:08:28 +00:00
duplicates
Convert GenomeLocParser into an instance variable. This change is required
2010-11-10 17:59:50 +00:00
exceptions
Make Indel Realigner exceptions related to not enough space on disk or a too low file-handle limit UserExceptions.
2010-12-07 16:37:31 +00:00
fasta
Update Picard / sam-jdk at Tim's request.
2011-01-03 02:17:25 +00:00
file
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
2010-09-12 15:07:38 +00:00
genotype
Moving GLF code to archive
2011-01-15 22:42:42 +00:00
help
Excluding the QFunction log files from the set of files to delete on completion.
2010-11-18 20:22:01 +00:00
instrumentation
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
2010-09-12 15:07:38 +00:00
interval
Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.
2011-01-07 22:03:36 +00:00
pileup
Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.
2011-01-20 12:54:03 +00:00
report
Recent changes to the build system make the build system complain loudly about
2010-09-24 22:09:12 +00:00
sam
Reverting back to the old definition of QD because it works better with large numbers of samples. The new QD is relegated to a new annotation: sumGLbyD. Tweaks to the new HaplotypeScore based on evaluation with better QD calculation. The default qual threshold in GenerateVariantClusters is updated to be in line with the variant quality scores coming from the exact model.
2011-01-13 14:12:30 +00:00
text
GenotypeConcordance now prints interesting sites more nicely. RMDTrackBuilder is now uses the root class FeatureSource not BasicFeatureSource.
2010-10-20 00:29:02 +00:00
threading
Removing unused file
2011-01-20 13:03:55 +00:00
vcf
A significant refactoring of the ROD system, done largely to simplify the process of
2010-12-31 04:52:22 +00:00
wiggle
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
2010-09-12 15:07:38 +00:00
yaml
Updated from SnakeYAML 1.6 to 1.7.
2010-09-22 19:47:49 +00:00
BaseUtils.java
Added validator for phasing using read information, e.g., PacBio: ReadBasedPhasingValidationWalker
2011-01-05 20:05:56 +00:00
CardinalityCounter.java
Moved phasing-specific utilities to phasing sub-directory
2011-01-13 15:38:20 +00:00
DisjointSet.java
Moved phasing-specific utilities to phasing sub-directory
2011-01-13 15:38:20 +00:00
GenomeLoc.java
Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.
2011-01-20 12:54:03 +00:00
GenomeLocParser.java
Looking over the daily error log email made me realize that there were 2 implementations of vc.modifyLocation() - the correct one in VC that didn't require lazy loading the genotype data and the bad one in VCUtils that did. Removing the implementation in VCUtils and updating the code accordingly. Also, removing createPotentiallyInvalidGenomeLoc() since no one uses it anymore.
2010-11-26 18:40:34 +00:00
GenomeLocSortedSet.java
vastly improved progress meter that estimates % of work done and time until the job finishes and time remaining. Reordered GATK core initialization order -- intervals are created before the scheduler.
2011-01-12 17:32:27 +00:00
HasGenomeLocation.java
Incremental commit for distributed computation. Appears to work but has potential deadlock situation not yet debugged. Do not use yet.
2011-01-17 21:23:09 +00:00
HeapSizeMonitor.java
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
2010-09-12 15:07:38 +00:00
MalformedGenomeLocException.java
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
2010-09-12 15:07:38 +00:00
MathUtils.java
HaplotypeScore is revamped. It now uses reads' Cigar strings when building the haplotype blocks to skip over soft-clipped bases and factor in insertions and deletions. The statistic now uses only the reads from the filtered context to build the haplotypes but it scores all reads against the two best haplotypes. The score is now computed individually for each sample's reads and then averaged together. Bug fixes throughout. The math for the base quality and mapping quality rank sum tests is fixed. The annotations remain as ExperimentalAnnotations pending more investigation.
2011-01-05 00:28:05 +00:00
PathUtils.java
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
2010-09-12 15:07:38 +00:00
PreciseNonNegativeDouble.java
Moved phasing-specific utilities to phasing sub-directory
2011-01-13 15:38:20 +00:00
QualityUtils.java
Checking in everyone's changes to the variant recalibrator. We now calculate the variant quality score as a LOD score between the true and false hypothesis. Allele Count prior is changed to be (1 - 0.5^ac). Known prior breaks out HapMap sites
2010-08-05 14:12:19 +00:00
ReservoirDownsampler.java
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
2010-09-12 15:07:38 +00:00
SWPairwiseAlignment.java
SW-turbo. Kind of. This implementation is presumably equivalent to the old one (mathematically), but runs ~10 times faster: inner loops eliminated completely. The author of the original implementation should be sentenced to the galleys. Oh, that would be me...
2010-12-01 00:08:47 +00:00
SampleUtils.java
A more general method for specifying samples to act on from the command-line. Supports samples specified individually on the console, a file of samples, or regular expressions to select multiple samples.
2011-01-06 14:54:56 +00:00
SequenceDictionaryUtils.java
- Fix DepthOfCoverage so that, when it abuses the ROD system by instantiating a track in onTraversalDone, it also supplies the correct sequence dictionary and parser.
2010-11-15 20:34:04 +00:00
SimpleTimer.java
Final version of BAQ calculation. default gap open is 1e-4, a good sensitive value. Useful timer class SimpleTimer added. BAQ is now live.
2010-12-10 19:35:12 +00:00
Utils.java
For the fullCallingPipeline.q:
2011-01-20 22:34:43 +00:00
WilcoxonRankSum.java
Fix for NaNs in the rank sum tests.
2011-01-05 15:21:30 +00:00
package-info.java
Put a major.minor version into the GATK Javadoc for reading. Also,
2010-01-15 21:48:30 +00:00
8855f080c2