| .. |
|
annotator
|
Various code improvements based on FindBugs
|
2010-07-09 15:04:48 +00:00 |
|
concordance
|
part one of combining format and info header lines code into a single abstract class for Mark; plus some 'm' removals from access methods for Eric. Adding fixes for CombineVariants next.
|
2010-07-05 05:57:58 +00:00 |
|
coverage
|
this got left off my last commit
|
2010-06-25 02:42:44 +00:00 |
|
fasta
|
BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.
|
2010-05-20 14:05:13 +00:00 |
|
filters
|
Fix for Steve: genotype filters still want to see the values from the VC
|
2010-07-11 04:30:15 +00:00 |
|
genotyper
|
Various code improvements based on FindBugs
|
2010-07-09 15:04:48 +00:00 |
|
indels
|
Various code improvements based on FindBugs
|
2010-07-09 15:04:48 +00:00 |
|
qc
|
Now that we always reserve space for two read ends when collecting stats stratified by libraries, we need to check that the second end was indeed present; otherwise the pointer is null and this was causing an exception
|
2010-06-28 16:40:16 +00:00 |
|
recalibration
|
An addition for Sendu since he can't seem to tell when his CountCovariate jobs die in the middle of writing the CSVs. We now write an EOF marker at the end of the covariates table and look for it when reading in the file in TableRecalibrationWalker. By default, we warn the user if the EOF marker isn't present, but we exception out if the user provides the --fail_with_no_eof_marker option.
|
2010-06-29 18:50:07 +00:00 |
|
sequenom
|
Update to PickSequenomProbes: Option to ignore mask sites within X bp of a variant (very useful for indels where dbSNP entries near the indel are almost always false SNP calls). Also fixed an integration test where the variant site itself, being in dbSNP, was represented as [N/C] rather than [A/C]. Added integration test for 1bp no-mask window.
|
2010-07-09 04:03:19 +00:00 |
|
varianteval
|
Fixes to VE for obscure bug, as well as disabled integration test for CombineVariants
|
2010-07-09 00:13:07 +00:00 |
|
variantrecalibration
|
--fdr_filter_level isn't mandatory
|
2010-07-08 22:48:30 +00:00 |
|
variantutils
|
Improvements for Jason
|
2010-07-09 20:18:37 +00:00 |
|
Allows.java
|
@Required / @Allows flags for main arguments.
|
2009-05-19 23:26:17 +00:00 |
|
By.java
|
Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along
|
2009-05-15 21:02:12 +00:00 |
|
ClipReadsWalker.java
|
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
|
2010-05-19 23:27:55 +00:00 |
|
DataSource.java
|
Framework for ROD walkers -- totally experiment and not working right now
|
2009-09-12 19:13:15 +00:00 |
|
Downsample.java
|
Experimental versions of downsampler and Ryan's deduper are now available either
|
2010-05-19 05:40:05 +00:00 |
|
DuplicateWalker.java
|
Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end.
|
2010-05-26 22:12:25 +00:00 |
|
FixBAMSortOrderTag.java
|
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
|
2010-05-19 23:27:55 +00:00 |
|
FlagStatWalker.java
|
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
|
2010-05-19 23:27:55 +00:00 |
|
LocusWalker.java
|
GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line
|
2010-06-02 22:26:32 +00:00 |
|
PileupWalker.java
|
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
|
2010-05-19 23:27:55 +00:00 |
|
PrintRODsWalker.java
|
Moving over to VariantContext from Variation
|
2010-04-19 06:56:29 +00:00 |
|
PrintReadsWalker.java
|
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
|
2010-05-19 23:27:55 +00:00 |
|
RMD.java
|
the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.
|
2010-03-31 22:39:56 +00:00 |
|
ReadFilters.java
|
Better support for specifying read filters to apply directly from the walkers.
|
2009-07-09 23:59:53 +00:00 |
|
ReadPairWalker.java
|
For Sarah Calvo: initial implementation of read pair traversal, for BAM files
|
2010-03-21 23:22:25 +00:00 |
|
ReadWalker.java
|
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
|
2010-05-19 23:27:55 +00:00 |
|
RefWalker.java
|
Added REFERENCE_BASES required annotation for performance
|
2009-06-18 21:03:57 +00:00 |
|
Reference.java
|
Windowed access to the reference.
|
2009-08-05 16:29:15 +00:00 |
|
Requires.java
|
@Required / @Allows flags for main arguments.
|
2009-05-19 23:26:17 +00:00 |
|
RodWalker.java
|
Framework for ROD walkers -- totally experiment and not working right now
|
2009-09-12 19:13:15 +00:00 |
|
SplitSamFileWalker.java
|
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
|
2010-05-19 23:27:55 +00:00 |
|
TreeReducible.java
|
N-way parallelism. Works for small test cases. Untested for large test cases.
|
2009-05-01 19:34:09 +00:00 |
|
VariantsToVCF.java
|
Thanks to Guillermo, I found a bug in the Unified Genotyper output: GL was posteriors instead of likelihoods. Not a huge deal because the
|
2010-05-28 19:28:26 +00:00 |
|
Walker.java
|
Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end.
|
2010-05-26 22:12:25 +00:00 |
|
WalkerName.java
|
Make command-line arguments available in walker constructor, provide back door from
|
2009-03-26 20:45:27 +00:00 |
|
Window.java
|
Windowed access to the reference.
|
2009-08-05 16:29:15 +00:00 |
|
package-info.java
|
Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file
|
2009-12-04 20:08:41 +00:00 |
6b960bd9c5