| .. |
|
arguments
|
Choose whether to keep program records based on Walker
|
2012-08-03 09:54:16 -04:00 |
|
contexts
|
Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.
|
2012-06-15 15:55:03 -04:00 |
|
datasources
|
Add removeProgramRecords argument
|
2012-08-01 15:33:05 -04:00 |
|
downsampling
|
Make downsampler classes themselves generic (instead of just the Downsampler interface)
|
2012-06-13 16:43:39 -04:00 |
|
examples
|
Adding categories for the remaining uncategorized walkers
|
2012-07-30 11:35:08 -04:00 |
|
executive
|
Sorting out HMS error handling (fingers crossed)
|
2012-07-25 23:13:12 -04:00 |
|
filters
|
Updating Read Filter documentation
|
2012-07-25 15:05:47 -04:00 |
|
io
|
Fixed older GS reported bug. Actually, the problem really lies in Picard (can't set max records in RAM without it throwing an exception, reported on their JIRA) so I just masked out the problem by removing this never-used argument from this rarely-used tool.
|
2012-07-31 16:00:36 -04:00 |
|
iterators
|
ActiveRegionWalker's isActive function returns a results object now instead of just a double.
|
2012-07-27 11:01:39 -04:00 |
|
phonehome
|
Maximum wait for GATK run report upload reduced to 10 seconds
|
2012-07-31 08:11:02 -04:00 |
|
refdata
|
Allele refactoring checkpoint #3: all integration tests except for PoolCaller are passing now. Fixed a couple of bugs from old code that popped up during md5 difference review. Added VariantContextUtils.requiresPaddingBase() method for tools that create alleles to use for determining whether or not to add the ref padding base. One of the HaplotypeCaller tests wasn't passing because of RankSumTest differences, so I added a TODO for Ryan to look into this.
|
2012-07-27 15:48:40 -04:00 |
|
report
|
Missing/malformed GATK report files are user errors
|
2012-08-02 11:33:21 -04:00 |
|
resourcemanagement
|
First pass of the asynchronous block loader.
|
2011-11-18 15:02:59 -05:00 |
|
samples
|
Added function to get founders IDs in SampleDB
|
2012-04-25 12:49:36 -04:00 |
|
traversals
|
ActiveRegionWalker's isActive function returns a results object now instead of just a double.
|
2012-07-27 11:01:39 -04:00 |
|
walkers
|
Bugfix for incorrect allele counting in IndelSummary
|
2012-08-01 15:45:12 -04:00 |
|
CommandLineExecutable.java
|
Old -B syntax is long gone at this point. Safe to remove the warning.
|
2012-04-02 22:25:16 -04:00 |
|
CommandLineGATK.java
|
Quick fix to user error catching
|
2012-07-31 15:50:32 -04:00 |
|
DownsampleType.java
|
…
|
|
|
DownsamplingMethod.java
|
…
|
|
|
GenomeAnalysisEngine.java
|
Choose whether to keep program records based on Walker
|
2012-08-03 09:54:16 -04:00 |
|
ReadMetrics.java
|
Counts of records failing filters are displayed sorted
|
2011-10-06 18:42:26 -07:00 |
|
ReadProperties.java
|
Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.
|
2012-06-15 15:55:03 -04:00 |
|
WalkerManager.java
|
Removed support for walkers ending with "Walker" from the engine.
|
2012-07-20 17:27:11 -04:00 |
|
package-info.java
|
…
|
|
524d7ea306