| .. |
|
arguments
|
Public-key authorization scheme to restrict use of NO_ET
|
2012-03-06 00:09:43 -05:00 |
|
contexts
|
Get rid of support for bams without sample information in the read groups. This hidden option wasn't being used anyways because it wasn't hooked up properly in the AlignmentContext.
|
2011-11-05 23:54:28 -04:00 |
|
datasources
|
BAMScheduler: detect contigs from the interval list that are not in the merged BAM header's sequence dictionary
|
2012-03-09 15:20:16 -05:00 |
|
examples
|
@Hidden for DocumentationTest and GATKDocsExample
|
2011-09-23 09:03:37 -04:00 |
|
executive
|
Documentation request by Eric. At each stage of the GATK where filtering occurs, added documentation suggesting the goal of the filtering along with examples of suggested inputs and outputs.
|
2012-02-09 11:24:52 -05:00 |
|
filters
|
It wouldn't harm integrationtests if we had our logic right... :-)
|
2011-11-10 14:03:22 -05:00 |
|
io
|
Fixed long-standing bug in tribble index creation
|
2011-09-20 10:53:18 -04:00 |
|
iterators
|
BitSet implementation of the on-the-fly recalibration using the CSV format file.
|
2012-03-16 13:02:15 -04:00 |
|
phonehome
|
Capture the class of the exception in GATKRunReport
|
2012-03-14 12:16:22 -04:00 |
|
refdata
|
Simplified the interface for simple VCF header lines by making the VCFSimpleHeaderLine not abstract anymore - now any arbitrary header line with an ID (e.g. the contig and ALT lines) can be part of this class without having to define new classes. Also, renamed the 'named' header line to 'id' since that's more accurate.
|
2012-03-19 21:29:24 -04:00 |
|
report
|
GATK Report code cleanup
|
2012-03-19 11:53:57 -04:00 |
|
resourcemanagement
|
First pass of the asynchronous block loader.
|
2011-11-18 15:02:59 -05:00 |
|
samples
|
Corrected bug causing getChildrenWithParents() to not take the last family member into consideration.
|
2011-12-09 14:51:34 +01:00 |
|
traversals
|
UnitTests for ActivityProfile and minor ART cleanup
|
2012-03-14 17:26:37 -04:00 |
|
walkers
|
Simplified the interface for simple VCF header lines by making the VCFSimpleHeaderLine not abstract anymore - now any arbitrary header line with an ID (e.g. the contig and ALT lines) can be part of this class without having to define new classes. Also, renamed the 'named' header line to 'id' since that's more accurate.
|
2012-03-19 21:29:24 -04:00 |
|
CommandLineExecutable.java
|
Public-key authorization scheme to restrict use of NO_ET
|
2012-03-06 00:09:43 -05:00 |
|
CommandLineGATK.java
|
Weirdly, PicardException inherits from SAMException, which means that our specialty code for
|
2012-01-24 15:30:04 -05:00 |
|
DownsampleType.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
DownsamplingMethod.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
GenomeAnalysisEngine.java
|
On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.
|
2012-02-13 12:35:09 -05:00 |
|
ReadMetrics.java
|
Counts of records failing filters are displayed sorted
|
2011-10-06 18:42:26 -07:00 |
|
ReadProperties.java
|
On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.
|
2012-02-13 12:35:09 -05:00 |
|
WalkerManager.java
|
Removed support for RMD in @Requires and @Allows
|
2011-08-03 15:36:55 -04:00 |
|
package-info.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
2324c5a74f