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gatk-3.8/java/src/org/broadinstitute/sting/gatk/walkers
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ebanks 7a91dbd490 Renamed some of the column names in Ti/Tv and Concordance modules so that they are clearer. Removed ValidationRate module (it was busted). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3564 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-06-16 15:53:06 +00:00
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annotator Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept 2010-06-13 01:47:02 +00:00
concordance 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
coverage Changes to Depth of Coverage: 2010-05-26 03:39:22 +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 VFW now uses a ref window and thus is compatible with indels. 2010-05-21 15:59:42 +00:00
genotyper Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept 2010-06-13 01:47:02 +00:00
indels ooops, debug print now removed 2010-06-14 18:07:12 +00:00
qc slight change in output format 2010-06-15 14:52:04 +00:00
recalibration Update to the latest rev of the picard sharding patch. Includes updates reflecting 2010-06-06 20:33:21 +00:00
sequenom 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
varianteval 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
variantrecalibration quick update for a change I implemented for Ryan 2010-06-09 17:23:31 +00:00
vcf 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
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