| .. |
|
arguments
|
The sharding system now buffers reads, with a size determined by command-line argument. Will investigate whether/how this
|
2010-07-01 22:28:55 +00:00 |
|
contexts
|
Nearly finalize merging capabilities for CombineVariants. Support for dealing with inconsistent indel alleles at loci. Improvements to Allele and removal of addAllele to MutableGenotype. We are close to being able to merge all of 1000 genomes -- snps and indels -- into a single combined vcf
|
2010-07-02 13:32:33 +00:00 |
|
datasources
|
The sharding system now buffers reads, with a size determined by command-line argument. Will investigate whether/how this
|
2010-07-01 22:28:55 +00:00 |
|
examples
|
Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes
|
2010-02-05 21:47:54 +00:00 |
|
executive
|
IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.
|
2010-07-01 04:40:31 +00:00 |
|
filters
|
Re-allowing blacklist by read group id.
|
2010-06-16 19:45:44 +00:00 |
|
io
|
Refactored ArgumentDefinition to absorb functionality from ArgumentDefinition and ArgumentTypeDescriptor.
|
2010-06-30 18:37:58 +00:00 |
|
iterators
|
The sharding system now buffers reads, with a size determined by command-line argument. Will investigate whether/how this
|
2010-07-01 22:28:55 +00:00 |
|
refdata
|
VCF headers now can be set to a particular VCF version after creation, which converts the header lines to the appropriate encoding on output. Plus some clean-up of the code.
|
2010-07-01 05:32:14 +00:00 |
|
traversals
|
A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.
|
2010-06-20 04:42:26 +00:00 |
|
walkers
|
Nearly finalize merging capabilities for CombineVariants. Support for dealing with inconsistent indel alleles at loci. Improvements to Allele and removal of addAllele to MutableGenotype. We are close to being able to merge all of 1000 genomes -- snps and indels -- into a single combined vcf
|
2010-07-02 13:32:33 +00:00 |
|
CommandLineExecutable.java
|
Better error message when bam file / list file with wrong extension is
|
2010-06-03 17:52:48 +00:00 |
|
CommandLineGATK.java
|
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
|
2010-04-20 15:26:32 +00:00 |
|
DownsampleType.java
|
We're unable to make the naive deduper more worldly, so we're killing it instead.
|
2010-06-18 13:54:27 +00:00 |
|
DownsamplingMethod.java
|
We're unable to make the naive deduper more worldly, so we're killing it instead.
|
2010-06-18 13:54:27 +00:00 |
|
GATKErrorReport.java
|
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
|
2010-04-20 15:26:32 +00:00 |
|
GenomeAnalysisEngine.java
|
The sharding system now buffers reads, with a size determined by command-line argument. Will investigate whether/how this
|
2010-07-01 22:28:55 +00:00 |
|
Reads.java
|
The sharding system now buffers reads, with a size determined by command-line argument. Will investigate whether/how this
|
2010-07-01 22:28:55 +00:00 |
|
WalkerManager.java
|
Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:
|
2010-05-28 14:52:44 +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 |
61e2b2e39b