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Author SHA1 Message Date
ebanks 0311980668 The VariantAnnotator can now officially annotate genotype (FORMAT) fields. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3037 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 03:30:14 +00:00
hanna 9b61d95d9c Khalid found an out-of-memory condition with the new sharding system when 
merging lots of BAMs, and the fix is taking longer than I thought.  Disable
experimental sharding when merging until the fix is ready.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3036 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 02:43:46 +00:00
ebanks b8e8852b4f Better interface for the Annotator in how it interacts with VariantContext. 
Also, added a proof of concept genotype-level annotation (not working yet, almost there).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3035 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 20:41:57 +00:00
hanna 96662d8d1b Moving from GATK dependencies on isolated classes checked into the GATK 
codebase to a dependency on a jar file compiled from my private picard branch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3034 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 17:43:42 +00:00
aaron 8a5f0b746e some cleanup for the output system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3032 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 12:54:39 +00:00
rpoplin c78fc23ec5 Minor updates to output of variant optimizer. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3031 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 12:46:47 +00:00
ebanks 0247548400 Fixed one test and (temporarily) punted on another 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3030 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 06:22:48 +00:00
ebanks ee0e833616 Some significant changes to the annotator: 
1. Annotations can now be "decorated" with any arbitrary interface description - not just standard or experimental.
2. Users can now not only specify specific annotations to use, but also the interface names from #1.  Any number of them can be specified, e.g. -G Standard -G Experimental -A RankSumTest.
3. These same arguments can be used with the Unified Genotyper for when it calls into the Annotator.
4. There are now two types of annotations: those that are applied to the INFO field and those that are applied to specific genotypes (the FORMAT field) in the VCF (however, I haven't implemented any of these latter annotations just yet; coming soon).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3029 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 05:38:32 +00:00
rpoplin 58a31bab6a Variant optimizer now outputs VCF files via ApplyVariantClustersWalker. Documentation to be added to the wiki. It is ready to be used by other people but only with great caution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3028 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 20:41:42 +00:00
hanna d9398dc347 Remove some of the restrictions on getStart() and getStop(); getStart() and getStop() 
now do the minimum validation rather than the more rigorous only-within-the-contig-bounds 
header validation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3027 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 19:39:30 +00:00
aaron 182f1061ff Bamboo isn't picking up commits for some reason; updating a copyright to see if it'll get this commit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3025 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 17:56:48 +00:00
ebanks 5e29d0c219 Be smarter about dealing with infinite quals for ref calls 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3024 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 17:35:23 +00:00
rpoplin 1bb4394aa9 Adding a skeleton for the second step of the variant optimization process. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3023 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 17:03:40 +00:00
ebanks ded4ba8966 Let's make artificial reads that actually adhere to the specs... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3022 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:51:42 +00:00
bthomas 5b34bb9ab0 Adding three minor new features: 
+ -L all now walks over all intervals

+ if a -L argument is passed with a .list extension, and file does not exist, returns a \
File Not Found error instead of "bad interval" error. We plan to soon revisit interval \
lists and generate a concrete list of filenames, so this is likely temporary.

+ Error is thrown if the start position on an interval is higher number than the end position.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3021 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:24:10 +00:00
ebanks 4340601c26 -Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically 
-Better integration test


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3020 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:00:10 +00:00
ebanks 76d14d17dc oops, need to update class names too 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3019 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 14:01:31 +00:00
ebanks 85a030069d renaming for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3018 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 14:00:28 +00:00
ebanks af5fd99444 Added filter for bad cigars (based on consecutive indels) - and cleaned up bad mates filter. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3017 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 13:53:42 +00:00
hanna 2cc040aa1c New sharding system is live. Disable with -ds. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3016 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 03:32:45 +00:00
ebanks 1fd909cdaf Fix for Kiran: -1 is a valid value for genotype qualities in VCF, so VariantContext shouldn't die. Cleaned up the relevant VCF code while I was in there. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3015 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 00:20:15 +00:00
hanna 849bd1f451 Set the eagerDecode flag in such a way that the binary data block in the BAM will always be considered dirty. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3014 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 22:01:23 +00:00
rpoplin 933823c8bc Removed the StingException when mkdir fails for Sendu in AnalyzeCovariates. Incremental updates to VariantOptimizer. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3013 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 19:45:02 +00:00
hanna 2525ecaa43 Oops. Commented out some tests to improve performance and then checked in the commented out tests. Reverted. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3012 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 16:34:50 +00:00
hanna 59045ccb28 Filter,merge performs much better than merge,filter. Many thanks to Eric for checking in an integration test that so compellingly demonstrates this. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3011 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 16:23:37 +00:00
hanna 6dd5f192e7 Performance improvements for RODs in conjunction with new sharding system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3010 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 14:54:12 +00:00
kiran f20f78d77f Don't crash if the tracker is null. Reset the alternate alleles based on the alts present in the subset of samples. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3009 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 04:00:04 +00:00
aaron 10e76abbbc adding some VE2 report infrastructure; work-in-progress. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3008 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 03:57:42 +00:00
ebanks 586f87fa35 Quick fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3007 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 02:59:26 +00:00
ebanks 202231141c -Push the --use_original_qualities argument into the engine. 
-Check that base and qual strings are the same lengths
-Fix one more bug in the clipper.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3006 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 02:06:11 +00:00
ebanks 035d4170aa fix bug in read clipper: output bam can be null, so check for it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3005 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 18:49:26 +00:00
ebanks 411d25c8d1 -Integration tests for walkers that use original quals. 
-framework for pushing -OQ into GATK (not done)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3004 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 18:46:31 +00:00
aaron e365d308d4 add a new JEXLContext that lazy-evaluates JEXL expressions given the VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3003 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 16:00:55 +00:00
kcibul 9f519af06d new method to filter out overlapping PE reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3002 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 15:40:09 +00:00
hanna 45f70de6df Fixed bug that failed to reset an accumulator when crossing contig boundaries, 
meaning that in special cases of shallow coverage, an interval might get dropped.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2999 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 04:45:55 +00:00
ebanks 73d6167bd6 Fixing broken integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2998 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-14 23:18:49 +00:00
depristo 4dd7c5972c Unit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2997 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-14 21:08:14 +00:00
ebanks e367a50e9b Added genotype concordance module. Not at all finished, but needed to give something to Aaron to look at for help in printing the output nicely. 
Also misc cleanup and fixes (e.g. perform evalulation even when no comp tracks are provided).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2996 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-14 19:02:24 +00:00
aaron ecb59f5d0d removed old tests and old code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2995 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 22:57:01 +00:00
depristo e7eae9b61d High performance, correct implementation of -XL exclusion lists. Enjoy. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2994 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 22:39:20 +00:00
aaron 88a48821ea removed the dependence on removeRegion() in GenomeLocSortedSet 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2993 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 22:35:49 +00:00
depristo b39b5edca8 Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2991 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 19:23:12 +00:00
aaron 1eb5f97255 fixed dropping single base intervals from deleteRegion, moving onto performance fixes. 
(stop - start is length-1 on closed intervals, so we need to check greater than OR equals to zero)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2990 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 19:14:21 +00:00
hanna 7aa7a5f9b8 Bug fixes for edge cases and filtration in the earlier performance fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2989 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 04:46:08 +00:00
hanna 5e8654fcdc Oops! Introduced a performance bug in read interval sharding, when the new sharding system is available. Track more state to avoid this problem in the future. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2987 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 23:19:42 +00:00
asivache d804bdf210 New option: --maxReadsInRam . When using ON_DISK sorting option, the tool may still run out of memory in the regions of pathologically deep coverage because of the generous memory usage limit set in the underlying samtools' sorting sam writers. With this option, the user can lower the number of reads the writer keeps in memory before spilling them on disk. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2985 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 21:15:03 +00:00
aaron 661a043cef adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2984 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 21:13:39 +00:00
depristo 18ba9929f9 notes for eric 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2983 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 20:34:54 +00:00
hanna cbd529d544 Better chopping up of data for ref walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2982 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 20:13:26 +00:00
hanna a7ba88e649 Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 
with less memory consumption.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2981 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 18:40:31 +00:00
ebanks 4a05757a2a Fixed strand bias calculation because of -Infinity issues. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2980 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 16:05:51 +00:00
aaron dde9fd8a15 some rods-for-reads cleaning and performance improvements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2979 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 22:54:58 +00:00
depristo 4f4555c80f PPV and Sensitivity added to validation tool output; support for arbitrary -sample arguments to subset variant contexts by sample 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2978 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 22:28:31 +00:00
ebanks 40d305bc7e Added test of Nway cleaning for Matt; thanks to Aaron for the help. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2977 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 21:00:41 +00:00
depristo 486bef9318 Support for validationRate calculation in variant eval 2; better error messages for failed genome loc parsing; tolerance to odd whitespace in plinkrod, and fix for monomorphic sites in vcf2variantcontext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2976 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 16:25:16 +00:00
ebanks c85ed1ce90 Plumbing is now in place to emit indel calls from the UnifiedGenotyper. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2975 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 04:30:12 +00:00
ebanks 5c35be39ef Now that extended events work for reference traversals, turn it off in the genotyper for non-indel models (thereby fixing busted integration tests). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2974 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 03:14:06 +00:00
ebanks 7ddd45d059 Hmm. I thought I removed this already. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2973 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 03:09:13 +00:00
ebanks 1a576525e9 misc improvements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2972 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 03:00:28 +00:00
ebanks 6e855809e1 Renaming and moving relevant tools into a sequenom directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2971 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 02:31:10 +00:00
asivache c638c29eea In reference traversals, this view did not expect a possibility of TWO alignment contexts (base pileup followed by extended event pileup) associated with the same location. As the result, extended event pileups were silently skipped even when enabled in the traversal engine. Fixed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2970 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 22:18:44 +00:00
ebanks bc3761dc16 allow clipper to use original quals if requested 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2969 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 21:50:31 +00:00
ebanks f096a958d6 Initial commit for Andrey of plumbing for indels. Not finished - need to track down bug with him. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2967 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 19:13:01 +00:00
chartl 0a49dffa8f Row/Column names are now R-friendly 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2966 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 19:01:03 +00:00
ebanks 0e360ea8af Alleles now hash correctly. 
Special thanks to Matt & Aaron.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2965 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 18:09:44 +00:00
ebanks e5475a7ba9 re-enabling PlinkToVCF integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2964 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 17:35:49 +00:00
ebanks 5a20bf0e64 3 changes to UG which break integration tests: 
1. emit AA,AB,BB likelihoods in the FORMAT field for Mark
2. remove constraint that genotype alleles (in the GT field) need to be lexigraphically sorted.
3. Add bam file(s) used by genotyper to header for Kiran


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2963 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 17:16:47 +00:00
hanna cdce639bae Partially reclaim performance lost during integration test fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2961 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 12:36:11 +00:00
ebanks 9f3b99c11b Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system. 
Removing obsolete genotyping classes.
First stage of removing dependence on old Genotype class.
More changes to come.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2960 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 03:41:07 +00:00
hanna 02f48b6457 Fix bug that's been in the GATK for a very long time: update nReads (as well 
as nRecords), so that INFO logging doesn't say 'skipped 0 of 0 reads'.  While
I'm in there, update TraversalStatistics to store longs.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2959 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 22:44:54 +00:00
chartl bca9bdcc68 Add integration test for quartiles overflowing on interval reduce 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2957 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 16:18:45 +00:00
chartl 21bf8b4b93 Odd, what I saw on IntelliJ hadn't saved to sting before committing. Here's the actual change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2956 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 15:54:41 +00:00
rpoplin fe8a8b9199 Hooked up both optimization models via command line arguments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2955 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 14:49:59 +00:00
chartl cc6a714c09 Handle excess coverage in interval output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2954 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 14:40:05 +00:00
rpoplin ca2a0266dc Converting annotation values that are set to Double.Infinity 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2953 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 14:04:33 +00:00
rpoplin b42e0a398e Bug fix in variant optimizer for when there are more novel variants than known variants in the callset. Changing the magic numbers related to the starting sigma values for the gaussian clusters. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2952 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 13:02:08 +00:00
hanna e4360bac6a More comprehensive support when sharding for ref walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2951 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 11:25:20 +00:00
hanna eb165ca844 Celebrate the fact that the new sharding system works with integration tests 
by removing the scary debug line.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2950 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 23:40:56 +00:00
hanna 9e107513d0 In the new sharding system, if no read group is present, hallucinate one. Added 
for test compatibility, but not sure whether we still need this feature.  TODO: Poll the group about this feature.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2949 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 23:01:34 +00:00
hanna a7fe07c404 A few stopgap fixes to get the GATK to the point where the old sharding 
infrastructure can be torn down:
1) New sharding system emulates old MonolithicSharding mechanism.
2) Better awareness of differences between fasta and BAM files when creating
   shards.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2948 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 21:01:25 +00:00
hanna dd6122f682 Fixed another bug in the original sharding system. Updated integration tests 
as appropriate.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2947 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 15:32:18 +00:00
hanna ee2ec7ced9 Fix off-by-one error in original implementation of read sharding. Tested by 
awking output of BamToFastq vs. samtools until the outputs matched exactly.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2945 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-06 18:52:53 +00:00
hanna 1ef1091f7c Cleanup and simplification of read interval sharding. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2944 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 23:34:38 +00:00
depristo ee913eca07 Forgot to check in fix this morning 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2943 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 21:07:19 +00:00
ebanks 7fa0f77721 add output for number of variants that validated as true 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2942 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 18:57:44 +00:00
chartl 037ac9c9af Actually calculate base counts by read group when "both" is specified. Modified integration test to cement the now-correct "both" behavior. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2941 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 18:31:48 +00:00
chartl 8738c544f1 Minor refactoring of CoverageStatistics to allow simultaneous output of per-sample and per-read group statistics. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2940 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 17:06:52 +00:00
rpoplin 95d560aa2f More incremental updates to the variant optimizer. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2939 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 16:42:42 +00:00
hanna 7a7e85188c Better eagerDecode default. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2938 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 16:42:23 +00:00
depristo 33cefddf55 Better INFO field annotation for Mendel violations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2937 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 15:22:04 +00:00
ebanks 9f7ebe1e1c - add name to vcf od field 
- don't do HW calculation if everything is a no-call


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2936 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 01:43:01 +00:00
hanna 7104a3a96c Fix for accumulator exception when running reduce by interval walkers without 
intervals.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2935 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 01:04:08 +00:00
aaron 366771d5a6 another test-with-multiple outputs fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2934 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 22:46:15 +00:00
ebanks 9eb122924f misc cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2933 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 21:34:13 +00:00
chartl 706d49d84c Commit for Aaron 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2932 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 21:29:07 +00:00
ebanks c20d3e567e Now outputs fully spec-compliant VCF with proper annotations. Emits statistics as to number of good/bad records. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2931 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 21:28:17 +00:00
aaron 54f04dc541 forgot to uncomment the auto-deletion of temp files... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2930 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 20:29:42 +00:00
aaron 80cc6bbeb4 add a way to test files generated by a walker that aren't command-line arguments; added some example code in CoverageStatisticsIntegrationTest for Chris. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2929 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 20:20:58 +00:00
hanna adea38fd5e Sharding system fixes for corner cases generally related to lack of coverage 
in the BAM file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2928 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 18:59:21 +00:00
chartl a4d494c38b Add option to adhere to the PlinkRod naming convention [ProjectName]|c[Chrom]_p[Pos] 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2927 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 18:31:27 +00:00