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gatk-3.8/java/src/org/broadinstitute/sting/gatk/walkers
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ebanks c6ad26e04f 1) When quals/GQs are really integers (x.00), strip off the floating points. 
2) Keep track of whether vcf records are unfiltered vs. pass filters in the variant context so we can regenerate the records on output.
3) No more "ID" hard-coded all over the code to set the VariantContext ID.  Use a static variable instead.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3840 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-07-20 18:01:45 +00:00
..
annotator 1) When quals/GQs are really integers (x.00), strip off the floating points. 2010-07-20 18:01:45 +00:00
concordance git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3775 348d0f76-0448-11de-a6fe-93d51630548a 2010-07-13 00:56:12 +00:00
coverage The first step in integrating Jim's tree based index scheme: 2010-07-19 04:49:27 +00:00
fasta FindBugs fixes throughout the code base 2010-07-18 16:29:59 +00:00
filters The GATK no longer writes vcf3.3; welcome to the world of vcf4.0. Needed to fix a few output bugs to get this to work, but it's looking great. Much more still to come. Guillermo: hopefully this doesn't break your local build too badly. 2010-07-14 04:56:58 +00:00
genotyper 1) When quals/GQs are really integers (x.00), strip off the floating points. 2010-07-20 18:01:45 +00:00
indels 1) When quals/GQs are really integers (x.00), strip off the floating points. 2010-07-20 18:01:45 +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 Official parallel CountCovariates, passes all integration tests. Now poster-child example of parallelism in GATK (Matt H). Apparent general performance improvements throughout too. 2010-07-19 22:13:18 +00:00
sequenom 1) When quals/GQs are really integers (x.00), strip off the floating points. 2010-07-20 18:01:45 +00:00
varianteval 1) When quals/GQs are really integers (x.00), strip off the floating points. 2010-07-20 18:01:45 +00:00
variantrecalibration Removing more references to VCFRecord 2010-07-14 16:34:15 +00:00
variantutils FindBugs fixes throughout the code base 2010-07-18 16:29:59 +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 FindBugs fixes throughout the code base 2010-07-18 16:29:59 +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
FlagStatWalker.java FindBugs fixes throughout the code base 2010-07-18 16:29:59 +00:00
LocusWalker.java Remove stray commented out line 2010-07-19 19:14:39 +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 1) When quals/GQs are really integers (x.00), strip off the floating points. 2010-07-20 18:01:45 +00:00
Walker.java FindBugs fixes throughout the code base 2010-07-18 16:29:59 +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