delangel 473ec91633 a) Bug fix in VCFHeader parsing - Info fields were not being parsed properly, with the result that the Count field was not being properly displayed in records (e.g. if Count=0 for a particular field, the INFO tag was still being displayed as ...;Field=x;... instead of ...;Field;... ... b) Bug fixes and update to how we represent indels and other complex events in a VariantContext object. Convention is now that all events are left aligned, with the first variant context location marking the common base before an event occurs. However, alleles in a VC don't have the common base in all VC's. Two new functions are now part of VariantContextUtils: CreateVariantContextWithPaddedAlleles and CreateVariantContextWithTrimmedAlleles. Both take a VC as an input and create a VC as an output. Main flow is that a VCF reader would create a VC with trimmed alleles, all walkers would ideally work with these trimmed alleles, and then the VCF writer would pad back the alleles before writing. However, there are special cases where we need to pad alleles like for example when merging/combining VC's. Pending issues: - PED and DBSNP RODs have to be updated to create VC's for indels following the convention above. Changes will go in after Tribble location is moved and things are tested. - Need to verify Indel genotyper and other modules that create VC's with indels.- Wiki page describing convention above and how walkers should interpret indel VC's still needs updating/detailing. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3850 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-22 02:36:45 +00:00
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HLAcaller	Solid processing in base quality recalibrator now has several options for how to handle no calls in the color space. --ignore_nocall_colorspace is removed and replace by --solid_nocall_strategy. Fixed some of the @Deprecated tags in BaseUtils. LocusWalkers now filter out FailsVendorQualityCheck reads. HLA caller integration test bam file had bad vendor reads so its integration test changed.	2010-07-19 19:10:29 +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
duplicates	forgot to update md5s	2009-12-29 20:31:29 +00:00
poolseq	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00
validation	a) Bug fix in VCFHeader parsing - Info fields were not being parsed properly, with the result that the Count field was not being properly displayed in records (e.g. if Count=0 for a particular field, the INFO tag was still being displayed as ...;Field=x;... instead of ...;Field;...	2010-07-22 02:36:45 +00:00
vcftools	First step in major cleanup/redo of VCF functionality. Specifically, now:	2010-07-16 22:49:16 +00:00
ClipReadsWalkersIntegrationTest.java	-Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically	2010-03-17 16:00:10 +00:00
HapmapPoolAllelicInfoIntegrationTest.java	Hurrr -- this uses power as part of its output. Changes to the power calculation broke the md5s RIGHT AFTER I HAD FIXED THEM arghflrg.	2009-12-14 22:42:50 +00:00