| .. |
|
arguments
|
Support for detecting and automatically excluding reads reading into the adaptor sequence and, if desired, also only showing the first pair when two reads overlap in the fragment. Not enabled, an intermediate check in before updating and verifying the impact on locus walkers everywhere.
|
2010-05-30 18:00:12 +00:00 |
|
contexts
|
Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept
|
2010-06-13 01:47:02 +00:00 |
|
datasources
|
Proper exception chaining for troubleshooting Sendu's issue.
|
2010-06-15 01:38:36 +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
|
Fail fast if users try to parallelize a read walker.
|
2010-06-03 18:14:33 +00:00 |
|
filters
|
Fixed read group blacklist filter to look only at readgroups (and not the read's themselves). Otherwise, it fails when attribute tags with different meanings show up in both places (e.g. SM). Added performance improvement.
|
2010-06-16 19:14:37 +00:00 |
|
io
|
Fixed UG parallelization bug. Better integration test to catch this in the future.
|
2010-05-25 21:03:45 +00:00 |
|
iterators
|
Reenabled downsampling by sample after basic sanity testing and fixes of the
|
2010-06-16 17:23:27 +00:00 |
|
refdata
|
a) Cleanup, remove -input argument from BeagleOutputToVCFWalker since it's not needed.
|
2010-06-16 02:13:08 +00:00 |
|
traversals
|
Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept
|
2010-06-13 01:47:02 +00:00 |
|
walkers
|
Renamed some of the column names in Ti/Tv and Concordance modules so that they are clearer. Removed ValidationRate module (it was busted).
|
2010-06-16 15:53:06 +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
|
Experimental versions of downsampler and Ryan's deduper are now available either
|
2010-05-19 05:40:05 +00:00 |
|
DownsamplingMethod.java
|
Experimental versions of downsampler and Ryan's deduper are now available either
|
2010-05-19 05:40:05 +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
|
Adding new support for reference data. ReferenceDataSource is a new class that manages reference data, and allows IndexedFastaSequenceFile to be a simple reader. This checkin also includes FastaSequenceIndexBuilder, which reads a fasta file and creates an index, like samtools faidx. Right now this is not enabled, because we are still working out thread safety. So the only new UI change is that GATK can be run without a fai file. Soon, we will enable 1) GATK to be run without a dict file too, and 2) both dict and fai files will be saved on disk for future program executions. For more info, see ReferenceDataSource.java
|
2010-06-10 20:10:23 +00:00 |
|
Reads.java
|
Experimental versions of downsampler and Ryan's deduper are now available either
|
2010-05-19 05:40:05 +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 |
d7f3102c3f