zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
4,766 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

3921 Commits (db55b2b0c6a34d75fa04196acbe1df4db9fa5d2b)

Author SHA1 Message Date
ebanks 1b3fc8ddd2 Doing things too quickly is also naughty. Thanks, Andrey. Now, we're even. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4597 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-29 14:50:04 +00:00
ebanks 58f7b4c595 Naughty use of assertions means that malformed records are not caught. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4596 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-29 14:41:38 +00:00
delangel 9a60e72364 Trivial change to LeftAlignVariants: make walker return number of aligned variants on map(), and print out the # of aligned variants at the end of the traversal. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4595 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-29 02:03:36 +00:00
hanna 2f8057bf24 Cleanup for multithreading memory leak during integration tests...unregister MXBean at end 
of traversal to avoid holding a reference to the microscheduler, which holds a reference to
the engine, which in turn holds a reference to the walker, which itself holds a reference to
all the data aggregated during the course of the traversal.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4594 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-28 18:37:42 +00:00
depristo 860de05a7c Bug fix for PL vs. GL in header. PL now truly default output for UGv2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4592 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-28 12:39:18 +00:00
depristo 9782dde3dd Bug fix for PL vs. GL in header. PL now truly default output for UGv2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4591 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-28 12:38:48 +00:00
ebanks fe3cfb067c very minor cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4590 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-28 02:11:33 +00:00
depristo cbce3e3c83 General support for both GL (log10) and PL (phred-scaled) genotype likelihoods. All walkers now use the Tribble GenotypeLikelihoods object for parsing VCFs with genotype likelihood fields. Please use GenotypeLikelihoods object from now on for seamless support for GL and PL tags. UGv2 now uses PL by default. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4589 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-28 01:48:47 +00:00
fromer 15183ed778 Reduced header to single sample when useSingleSample arg is given (to prevent lots of pointless no-calls) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4588 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 23:02:10 +00:00
fromer 34538bf2b3 Added ability to focus only on a single sample and/or emit only merged records in MNP merger 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4587 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 20:41:05 +00:00
kshakir 5cdd7a7ba4 There's no such thing as a sam index, so the GATK extension generator doesn't need to add an @Input for them. 
Updated a call to swapExt to specify the directory.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4586 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 20:39:03 +00:00
hanna 4c23b1fe9c Get rid of the static cache of ArgumentTypeDescriptors by making them an integral part of the 
parsing engine.  Hugely lowers our memory footprint in integrationtests, but not yet enough to 
run Mark's new parallelized VariantEvalIntegrationTests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4585 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 19:44:55 +00:00
ebanks e112df20df Use a sorting VCF writer because records can flip positions during left-alignment 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4583 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 06:33:03 +00:00
ebanks 708e973911 Adding a walker to left-align indels in a VCF file (was able to reuse code from AlignmentUtils to do the hard part). The code correctly updates the alleles if they change. This makes it much easier to compare our indel calls to e.g. CG or dbSNP. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4582 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 06:08:26 +00:00
ebanks ec442086ec Minor refactoring of the cleaner allows me to add a trivial walker that left aligns the indels present in reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4581 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 03:39:10 +00:00
hanna 04e38929f0 Disabling parallelized version of VE integration tests. Still slow, but not 
deadlocking any more.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4580 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 02:47:03 +00:00
ebanks ffc0ed2b32 Renamed getName() to getSource() in VariantContext to be more accurate 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4579 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 02:21:41 +00:00
ebanks 52fc023d80 Added convenience methods to check/get the ID of the VariantContext 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4578 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 01:56:58 +00:00
fromer a7af1a164b Updated MNP merging to merge VC records if any sample has a haplotype of ALT-ALT, since this could possibly change annotations. Note that, besides the "interesting" case of an ALT-ALT MNP in a pair of HET sites, this could even occur if two records are hom-var (irrespective of using phasing). Note also that this procedure may generate more than one ALT allele. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4577 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 01:50:36 +00:00
depristo e02aac0743 No longer print out 0 reads were filtered out... message when there were no reads scene at all 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4575 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-26 20:22:16 +00:00
depristo b085648141 Parallelized VariantEval. Refactored output to support parallel output style. Minor improvements to testing framework to enable easy executeTestParallel to run -nt 1 and -nt 4 by default. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4574 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-26 20:21:38 +00:00
kshakir 8211cee0b2 Queue UI Improvements: 
- Forcing user to set the temp directory via -Djava.io.tmpdir to avoid filling up /tmp.
- By default deleting job outputs tagged as intermediate.
- Defaulting pipeline to scatter count 1 (no reads deleted).
- Cleaning up temp classes even when scripting fails.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4573 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-26 19:49:08 +00:00
ebanks cedceb33cd My only experience with getting external groups (GAP,dbSNP) to use VCF has been painful at best, so I'm not holding my breath to get indels for CG in VCF. To that extent, here's a oneoffs walker to convert from CG format to VCF for all 'del' & 'ins' types (but not 'sub' types, since they're too complex to code up in VCF and I don't care about them for now). rs ids are included. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4572 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-26 17:53:14 +00:00
ebanks 071799453c More complete fix to previous commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4571 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-25 20:47:37 +00:00
ebanks 67a776d53c Yikes! VariantEval was always loading genotypes unnecessarily when no sample list was provided because the order of the checks in the if statement wasn't optimal. This results in a massive performance penalty when running with many-sample VCFs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4570 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-25 20:30:23 +00:00
ebanks 0d97394c4f Add capability to liftover to do the right thing when sections of the genome are reverse complemented. This does not work for indels (we don't try to reverse complement) because we need to figure out what the hell to do about the fact that the 'base to the left' that we automatically add on will be wrong because the location of the indel actually changes when reverse complemented. Sheesh. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4569 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-25 20:03:03 +00:00
fromer c357ec775a Trivially phases any hom site (since it is always correct to continue the previous haplotypes by appending the same allele onto both haplotypes) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4568 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-25 16:58:41 +00:00
rpoplin da64183854 Fix for the case of the truth VCF file having multiple SNPs at the same locus. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4567 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-25 15:04:50 +00:00
hanna 3039c0de3c Retire old ROD syntax. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4564 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 23:52:11 +00:00
depristo 78e71c4167 Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4561 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 20:35:44 +00:00
fromer f06f955e06 Added count of number of mergeable records (within specified distance cutoff) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4560 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 20:11:15 +00:00
depristo 84b6d2926b Useful walker that creates a new interval list with only the interval overlapping input sites list. Really a one-off walker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4559 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 19:55:04 +00:00
depristo 78b4a1c240 VariantsToTable now supports the virtual TRANSITION field 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4558 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 19:53:46 +00:00
hanna e6d61197e6 Disable OTF indexing when writing indices for temporary VCFs when running 
with -nt option.  When last I checked in, Ryan was seeing a ~25% speedup 
per shard by not indexing.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4556 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 17:40:37 +00:00
depristo e6b008f87c Fixed >= vs. > test leading to failure to tolerate dynamic indexes that are created at *exactly* the instant the output VCF is closed too 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4555 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 16:11:14 +00:00
ebanks 72c5b75460 Tribble exceptions can be generated outside of the normal codec parsing code because we now lazy load the VCF genotype fields. I'm not sure how else to account for this (to make sure they show up as user errors and not GATK system errors) besides catching them here. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4554 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 15:22:17 +00:00
delangel e24f7fec47 Fixed indel genotyper which broke yet again because we can't just call context.getBasePileup() without checking again for its existence in the first place. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4553 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 15:17:11 +00:00
ebanks c0b4317311 Er, here's the right fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4552 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 15:08:25 +00:00
ebanks 181f901126 Fix for Ryan: don't pull reference sequence for the portions of reads that extend beyond the contig boundaries 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4551 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 14:38:26 +00:00
ebanks 9f76aed515 Fix for IDs 5zP7jJeffK2sdPH1BH4JBVSrQztVEDKP and nX0cuBjoqBW4NQFpM6dE13KpkCuYFpZu 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4550 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 14:05:27 +00:00
hanna d4feb99d9a For parallel ROD traversals, simplified reference sharding. Will replace 
with a more sensible strategy for sharding w/o BAMs at some point after
ASHG.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4549 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 05:08:15 +00:00
fromer 9ba7269728 Fixed Integration Tests to output VCF files with -NO_HEADER 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4548 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 19:49:44 +00:00
fromer 60f88866dd Uses VCFConstants instead of hard-coded constants 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4547 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 19:49:01 +00:00
fromer 883b8ff80e Removed flush() method from VCFWriter interface; added takeOwnershipOfInner parameter in constructor of wrapper VCFWriters to designate if the Writer should close the inner Writer it receives on construction 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4546 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 19:48:00 +00:00
fromer 1ea43be976 Removed flush() method from VCFWriter interface 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4545 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 19:46:42 +00:00
chartl 3566ad2146 Wrong if statement. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4544 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 17:37:45 +00:00
chartl bf17f92b64 Do not look for samples in dbsnp binding 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4543 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 17:36:38 +00:00
ebanks 225cf49128 Implementing reference confidence estimate in UGv2 as per UGv1 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4542 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 16:57:59 +00:00
delangel cf9c9ae241 Three important updates for Dindel genotyper: 
a) Fix it up because it broke with a recent checkin to annotate vcf with unfiltered depth.
b) Printout of ref/alt alleles in output vcf was incorrect because the start/stop positions of associated GenomeLoc were incorrectly computed in case of a deletion.
c) Redid Beagle input/output walkers as not assume that ref was a single base, not to assume that variant was a vcf and generalized it to be indel-capable, so now the Beagle walkers can be used for indels as well.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4541 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 16:00:16 +00:00
kshakir b88cfd2939 Updated MD5s of VCFs, since the approximate command line arguments injected into the VCF headers now have a little more order to them thanks to changes in the ParsingEngine. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4538 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 03:07:40 +00:00
ebanks 8f38ebf98e Throw a user exception when using the clustered SNP filter in the presence of ref calls. It's unfortunate, but until we get a windowed ROD context this is just too much of a headache to support. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4537 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 02:44:10 +00:00
kshakir 88a0d77433 Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines. 
Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator.
Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered.
Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers.
Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 21:43:52 +00:00
ebanks 91049269c2 Optimizations across the board, with help from Guillermo, Matt, and JProfiler. Too tired to give details now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4535 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 20:47:41 +00:00
fromer f76865abbc ReadBackedPhasing now uses a SortedVCFWriter to simplify, and has the ability to merge phased SNPs into MNPs on the fly [turned off by default]; MergeSegregatingPolymorphismsWalker can also do this as a post-processing step; Integration tests for MergeSegregatingPolymorphismsWalker were also added 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4534 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 20:27:10 +00:00
fromer e8079399ac Added flush() method to VCFWriters 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4533 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 20:23:22 +00:00
fromer 00726b6c4b Added mergeIntoMNPs to merge successive VCF records into a single MNP VCF [if possible] 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4532 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 19:40:26 +00:00
fromer 55230ce5f3 Added startsBefore, startsAfter, and minDistance [calculates distance between any pair of bases in the two GenomeLocs] 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4531 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 19:12:34 +00:00
ebanks 4f77581087 More optimizations for HaplotypeScore: pulling final constants out of loops 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4530 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 17:40:57 +00:00
hanna 20fac43521 Add extra logging to the GATK run report at the start of metrics aggregation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4529 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 17:32:51 +00:00
ebanks a205900eff Naughty use of Strings in HaplotypeScore literally double the runtime of Unified Genotyper. Moved over to bytes and no longer allow Strings in the Haplotype util class. New round of profiling on tap for tomorrow. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4528 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 03:32:21 +00:00
depristo f9541b78d3 Timing of traversal now starts at the start of the traversal, so the rate is reasonable right off the bat. For example, we now see: INFO 22:45:02,476 TraversalEngine - [TRAVERSAL STARTING]; INFO 22:45:32,484 TraversalEngine - [PROGRESS] Traversed to 2:50850686, processing 18,646 sites in 30.05 secs (1611.50 secs per 1M sites) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4527 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 02:47:34 +00:00
depristo f7ce18553e GenotypeConcordance now prints interesting sites more nicely. RMDTrackBuilder is now uses the root class FeatureSource not BasicFeatureSource. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4525 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 00:29:02 +00:00
ebanks 7a291a8ff3 First pass at a VCF validator. Will test more tonight. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4524 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-19 19:55:49 +00:00
chartl 341e93ee12 The reference fixer seems to have munged the OMNI rather than making it better. Looks like some sites need to only have the ref and alt bases swapped, and others need to have the genotypes swapped as well? E.g. 
some subset need
A  C  1/1   -->  C  A  0/0

while another subset need
A  C  1/1   -->  C  A  1/1

it's unclear how big these subsets are (or even if one is empty). What I do know is, doing the first one totally screws up concordance metrics for the 421-sample chip. So either something else needs to be done, or there's a bug in this walker. Until I know for sure, I've added an initialize exception to disable this thing...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4523 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-19 12:50:24 +00:00
ebanks 5251f49a90 Including Marian Thieme's BaseCounts class (with some modifications) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4522 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-19 03:07:30 +00:00
hanna c5f105d050 Fix boneheaded mistake in the new interval filtering code I added on Sunday. 
Sorry everyone.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4521 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-19 01:20:12 +00:00
ebanks 524cb8257c Renaming for accuracy 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4519 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-18 18:11:07 +00:00
ebanks 0fe504b748 Use filtered depth for Exact model (just like grid search) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4518 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-18 18:08:31 +00:00
ebanks d54d9880d7 Now that G's new genotyping algorithm is live, I've cleaned up the code to completely separate the grid search from the exact model. AlleleFrequencyCalculationModel is now completely abstract. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4517 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-18 18:04:06 +00:00
ebanks 80e5ac65b4 CAP_BASE_QUALITY needs to be included in the clone() method for it to be usable in UG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4516 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-18 03:11:03 +00:00
hanna 6af9532090 Fix for GATK slowdowns at the ends of intervals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4514 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-17 23:21:23 +00:00
chartl 5889138f4a *facepalm* 
forgot to add the samples to the header. How could the VCFWriter let me get away with something so boneheaded?!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4513 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-17 05:36:29 +00:00
chartl 2bc5971ca1 Added - a tool to fix reference bases of a VCF. The OMNI had a couple of sites with incorrect reference bases (look to be legacy from other chips), and a few more that had ref and alt flipped. GAP should probably take care of it, but since I need results by monday, I'm doing it. 
Modified - SelectVariants: Hook up to VariantContextUtils to recalculate AC/AF/AN, which uses the accessor in VariantContext to do this. Somehow sites that were selected down to hom-ref genotypes only wound up getting positive AC. 

**IMPORTANT** I kind of need input here. The header of a file used for an integration test specifies AC as being an integer. Recalculating it casts it into an integer list (which it should be, as it allows for alternate alleles). However this appears to clash with what the jexl expression is looking for? For now, the integration test itself needed to be changed -- it's unclear what to do when the header specifies AC of being one class, but recalculating it casts to another class, and I'm not sure what to do.

I'm committing my omni_qc pipeline because I'm almost certain 2 months down the road I'm going to wonder what the heck I did to generate my results.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4511 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-17 03:18:01 +00:00
ebanks 7aa030a9a4 Hmm. Apparently variants can get lifted over to different chromosomes. Who knew? Reverting changes from a couple of days ago. The only way to do this correctly (without requiring lots of memory) is to turn off on-the-fly indexing for this walker. Integration tests cover this now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4510 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-17 02:54:12 +00:00
chartl 8b2d387643 Added in an eval module that calculates the dispersion histograms between eval and comp (e.g. M_{i,j} = # of times eval observed to have AC i, comp AC j -- for af it's i/100 vs j/100 ) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4507 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 19:07:43 +00:00
ebanks f78ff08e2b This is less correct than my previous change but it's what UGv1 does and now is not the right time to start mucking with things. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4506 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 18:56:45 +00:00
ebanks 471c18054f Fix for SB calculation: the best overall AF might not have any mass when just looking at reads from a single strand. We need to compute the best AF for each stratification. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4505 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 17:51:18 +00:00
asivache 42c3d74432 bug fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4503 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 16:27:40 +00:00
chartl c9d473edee More changes to Variant Eval and Genotype Concordance (passes all integration tests): 
1: -sample can now include a file, which will be parsed for sample-name entries
2: If you request a sample to run analysis on, but it is not present in any of your RODs, VEW will exception out
3: Change added to parse Integer, String, and List<Integer> type Allele Count annotations (error otherwise)
4 [slightly problematic]: The count objects now maintain row-keys in order, as the keys were taking an inordinate amount of time in onTraversalDone (multiple calls to getRowKeys(), so many multiple sorts of the same underlying unsorted object, very bad)

There is a legacy comparison object which is unused which I will strip out soon.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4502 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 12:40:36 +00:00
ebanks 954dd84f51 Adding an integration test (against hg18 this time) that requires on-the-fly sorting in order to work properly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4500 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 07:45:21 +00:00
ebanks 9f54170dff Hooking up the liftover tool to the new on-the-fly sorting VCF writer so that records can now get emitted in order. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4499 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 07:27:01 +00:00
ebanks d41c252b13 Looking over the calling results with Ryan, it's clear that while the grid search optimization (ignoring samples that are clearly ref) can work for assigning genotypes, it cannot be used for calculating P(AF>0). There's too much area under the likelihood curve that gets lost and the QUALs are negatively affected. However, testing showed that this only slightly affects runtime (~15 minutes per 1Mbase for the 1kg allpops). The optimization does remain for genotyping. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4498 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-14 19:06:32 +00:00
ebanks 2606e67cf1 Reverting Matt's change from yesterday which I accidentally blew away when trying to cope with the stupid svn update issues we've been plagued with recently. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4495 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-14 14:40:42 +00:00
ebanks cfb33d8e12 Filtering optimizations are now live for UGv2. Instead of re-computing filtered bases at every locus, they are computed just once per read and stored in the read itself. Eyeballing the results on the ~600 sample set from 1kg, we cut out ~40% of the runtime! QUALs are now sometimes different from UGv1 because I noticed a bug in v1 where samples with spanning deletions only were assigned ref calls instead of no-calls which ever so slightly affects the QUAL. Not a big deal though. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4494 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-14 05:04:28 +00:00
chartl 4ac636e288 Minor change: when tabulating concordance by AC, ignore sites with multiple segregating alleles in the population, at least for now 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4493 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-14 01:35:33 +00:00
chartl 7c9ef59d65 This is simultaneously a minor and major change to VariantEval, so take heed: 
The core walker has been modified so that when variant contexts (eval and comp) are subset to command-line-specified sample(s), the chromosome count annotations (AC/AN/AF) are altered to reflect the AC/AN/AF of only those samples involved in the comparison. No more getting AC500 when you're comparing a 10-sample overlap. Interestingly enough, this didn't break any integration tests.

GenotypeConcordance now has two additional tables: Allele Count Statistics, and Allele Count Summary Statistics. These work exactly identically to the Sample Statistics and Sample Summary Statistics tables, except that the partition being used is no longer the sample, but instead the allele count of the variant sites. These tables stratify by both eval and comp ACs, e.g.

evalAC0
evalAC1
evalAC2
compAC0
compAC1
compAC2

Differences with previous integration tests were verified to only be in the Allele Count tables (by grepping them out of the diff); a new test has been added for the simple case of an AC=1 site in the eval becoming an AC=2 site in the comp.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4491 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-13 22:26:15 +00:00
hanna 83b8676b69 Hack to fix mysterious disappearing read attributes. Ultimately caused 
by the fact that the GATKSAMRecord, by design, needs to both inherit from 
SAMRecord and wrap a 'member' SAMRecord, and method calls that aren't
implemented as explicit passthroughs can compromise the content of the
SAMRecord in subtle ways.

Will be automatically fixed when Picard moves to a lightweight SAMRecord
interface rather than the current heavyweight implementation.  But in 
the short-term, there's no obvious fix.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4489 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-13 19:06:54 +00:00
depristo da29fcdb68 No longer writes the index to disk twice. But fixes for closing VCFWriters throughout the codebase 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4488 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-13 14:26:06 +00:00
aaron 28a1020c89 comment out debugging line that was clogging the performance test output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4487 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-13 03:26:55 +00:00
aaron 272ac2ae4a more fixes for tests broken by indexing-on-the-fly; I think this should do it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4486 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-13 01:54:32 +00:00
hanna ed39af53cd Fix for exception when trying to load reference segment for a read that aligns 
to 0 bases.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4485 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-12 23:50:51 +00:00
ebanks fe9f128631 Better fix for earlier bug. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4484 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-12 19:21:33 +00:00
aaron ff0df1a2da A fix for an integration test that was broken by on-the-fly indexing. Also, better reporting of Tribble exceptions in GATK integration tests. Trying to get the tests back up and running... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4483 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-12 18:39:56 +00:00
ebanks 69652e08c6 Bug fix for reads that completely fall within an insertion: the I cigar string element was 1 base too long. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4482 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-12 14:46:21 +00:00
kiran f348ca2976 Now processes VCF files with repeated loci without crashing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4481 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-12 04:36:07 +00:00
ebanks fd8351cd49 Get rid of useless test/'optimization' that was carried over from UGv1. New codde is (minimally) faster with same results. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4478 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-11 04:04:07 +00:00
ebanks f28523e7de Implemented SB for UGv2. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4477 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-11 03:56:01 +00:00
hanna 7008a469dc Update MalformedReadFilter to pass reads that have cigar strings like 40S36I 
that have 0 aligned bases in the genome.  We'll have to fix walkers as faults
appear.

Also added JIRA GSA-406: finer-grained control of MalformedReadFilter: want
to exception out by default in these cases but pass them with a warning with
a corresponding -U flag.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4476 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-11 03:01:04 +00:00
ebanks 530875817f Experimental code for better filtering of bases in sam records. Not hooked up yet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4475 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-11 02:19:51 +00:00
ebanks a0de269c4b Better message 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4474 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-10 20:11:51 +00:00
rpoplin 0a4cf02a52 Fix for index out of bounds exception in VR. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4473 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-10 17:35:15 +00:00
depristo 116309b3c3 More test cases for UG integration test. We currently fail doing multi-threaded gzip output, FYI 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4472 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 20:22:12 +00:00
depristo 38a67fed63 High performance version of standard vcf writer. New general static Tribble class for common constants, including general .idx constant and functions to get standard index name for a given file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4471 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 19:53:21 +00:00
fromer bdd3a9752e Changed min MQ and BQ to 20 (for phasing) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4469 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 19:27:45 +00:00
asivache 05500d1a8d An iterator wrapper/adapter: takes GenomeLoc iterators 1 and 2 and traverses intersections of intervals from 1 with intervals from 2. Both 1 and 2 must be SORTED and NON_OVERLAPPING, but this iterator does NOT perfrom any checks, so if these conditions are not met, the behavior is unspecified 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4468 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 16:34:00 +00:00
asivache 253d528e49 not ready for commit yet 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4467 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 15:30:55 +00:00
asivache 4f2f33b42a fix method invocation to conform to new API; this version of the code will compile but new functionality is still not fully in 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4466 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 15:30:26 +00:00
asivache cece19d4d2 not ready for commit yet 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4465 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 15:14:54 +00:00
asivache 39e373af6e deleting accidentally committed junk 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4464 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 15:13:01 +00:00
asivache b3d81984aa renaming MergingIterator to RODMergingIterator as it is more appropriate for this specialized implementation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4462 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 14:10:11 +00:00
asivache 77dddd0afa renaming MergingIterator to RODMergingIterator as it is more appropriate for this specialized implementation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4461 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 14:08:28 +00:00
chartl 21ec44339d Somewhat major update. Changes: 
- ProduceBeagleInputWalker
 + Now takes a validation ROD and a prior to give it, will use those genotypes in place of the variant genotypes if both are present
 + Takes a bootstrap argument -- can use some given %age of the validation sites
 + Optionally takes a bootstrap output argument -- re-prints the validation VCF, filtering those sites used as part of the bootstrap
-BeagleOutputToVCFWalker
 + Now filters sites where the genotypes have been reverted to hom ref
 + Now calls in to the new VCUtils to calculate AC/AN

-Queue
 + New pipeline libraries for easy qscript creation, still a work in progress, but this is a considerable prototype
 + full calling pipeline v2 uses the above libraries
 + minor changes to some of my own scripts
 + no more need for contig interval lists, these will be parsed out of your normal interval list when it is provided



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4459 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 13:30:28 +00:00
ebanks 97b153f2fa Quick fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4457 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 06:10:52 +00:00
ebanks acd238f3f2 For Chris: pull out the chromosome counting code into VCUtils so that other tools can make use of it. Transitioned SelectVariants over to use it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4456 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 04:37:54 +00:00
delangel 3838823262 Two ugly hopefully temporary fixes for new genotyping model: 
a) In Indel genotyper: we can't deal yet with extended events correctly and we are still triggering at each extended event which results in repeated records on a vcf. So, to avoid this, keep track of start position of candidate variantes we've visited and if we've visited a variant before we don't do it again.
b) Avoid infinite terms in QUAL and in genotype likelihoods which can happen if posterior AF happens to be exactly zero. For now, hard-code a minimum value of each term of the posterior AF likelihood to be -300 (ie 1e-300 in lin space). This can be solved with better and smarter log-to-lin conversions and some precision fixes in AF calculation.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4455 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-08 00:53:16 +00:00
depristo 0a2e76e9dc 2nd step towards on the fly indexing. Also fixed parsing bug for headers with < symbols 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4454 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-07 21:38:46 +00:00
rpoplin 7bb9704592 Update the BeagleOutputToVCF integration test because of removing the source header line. Source headers are provided by the engine for all VCF files now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4453 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-07 19:55:57 +00:00
rpoplin 0de658534d Removed the qScale arguments in VariantRecalibrator. It is smarter about how it tries to find a cut so the arbitrary scale factor hopefully is no longer necessary. Now the recalibrated variant quality score more accurately reflects our believed lod of the call. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4451 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-07 18:04:57 +00:00
fromer ee00dcb79d 1. Phasing now ignores bases without minimum base quality (BQ) and minimum mapping quality (MQ); 2. The probability of a non-called base is now divided by 3, to evenly split up the error probability over the non-called bases 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4450 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-07 17:40:59 +00:00
ebanks 6205910f9f updating integration test for Sarah Calvo 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4449 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-07 04:03:37 +00:00
fromer 652a3e8de5 Added integration tests for ReadBackedPhasing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4446 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 20:50:32 +00:00
fromer f8f1cc45a3 Now ReadBackedPhasing caps Base Quality by Mapping Quality 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4445 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 20:48:57 +00:00
scalvo bda427f078 Change specification of AnnotationInputTable, and fix 2 bugs. 
Previous output spec contained 3 columns:
 haplotypeReference,haplotypeAlternate,haplotypeStrand
where haplotypeReference was always on the + strand, and haplotypeAlternate was on the strand specified by haplotypeStrand.

The new specification contains 3 columns:
 haplotypeReference,haplotypeAlternate,transcriptStrand
where haplotypeRef and haplotypeAlt are required to be on the + strand.  transcriptStrand now specifies the strand of the transcript, which is needed for interpreting the haplotypes.

Bugfix #1: fix incorrect assignment of variantCodon and variantAA
(Previously variantCodon was incorrectly set to referenceCodon)

Bugfix #2: fix incorrect codingCoordStr values for - strands (bug reported by Giulio Genovese), and incorrect usage of "m." for mitochondrial transcripts (bug reported by Steve Hershman)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4444 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 20:46:09 +00:00
scalvo b5c127e643 Removed HAPLOTYPE_STRAND_COLUMN; Previously, GenomicAnnotation allowed a user to specify the strand of the haplotypeAlternate, and would reverseComplement the haplotypeAlternate if HAPLOTYPE_STRAND_COLUMN was "-". The new specification does not allow this functionality, and instead requires both the reference and the alternate haplotypes to be on the + strand (as in VCF format). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4443 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 20:37:41 +00:00
kshakir ca5db821ce Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality. 
Queue now submits new LSF jobs only after previous functions have completed successfully.
When the Queue process is shutdown (ex: via Control-C) sends a bkill command for any running jobs.
Ported commands like creating directories and scatter/gather interval list to scala functions.
Updates to LSF status tracking by porting the python to internally generated bash scripts.
Temporarily disabled job name submission to LSF.  Plus side is that the full command is now available in "bjobs -w".  TODO: Put back jobName passing to LSF based on an option?
Changed BaseTest to allow scala to access paths to references.
Changed the extension generator to default the analysis name to the walker "name".

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4442 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 18:29:56 +00:00
ebanks 3c5dc675ab For Guillermo: only decide that something is a clear reference call if it is at least 10 times as likely as the next best genotype 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4441 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 15:16:41 +00:00
depristo 00491fcd2e Only see not writing GATK Run Report if you are running with debug enabled 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4437 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 14:09:21 +00:00
rpoplin 69485d6a7a Added command line argument for the max value of the allele count prior in VariantRecalibrator (--max_ac_prior). Default value increased to 0.99 from 0.95. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4436 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 14:00:53 +00:00
ebanks 3d564f4a29 reverting an accidental change from the dindel merge 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4434 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 03:08:09 +00:00
ebanks b5e148140b Officially fixed the UG priors; updated the default min MQ/BQs to pipeline values of q20 and min calling threshold to Q50 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4431 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-05 18:35:36 +00:00
fromer c6668bd49c Fixed bug in phasing, where mapping probability was incorrectly raised to the power of number of non-null bases [instead, it is just multiplied into phasing probability once] 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4430 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-05 17:07:31 +00:00
hanna 250c18e679 Error message fixes for the following issues: 
nvjpM4yOwQAu3fNGxi4oXLuVpKn6aAlf,1GL0OuXK2xKQfvbu34tWYgbojSVSLo0l,
ehEGBJOfgc4V7qj8W0Homf5ICuVK5Sm3,cZsreLm1CbY3aYKZhV7DOSvQNwur41zp,
GlrlyGEyP9kJDIRCQNFQp7BGJBXSzdDJ,hyz1uiHXr39ANmdZu9K1epOSX8EL3mDw,
q0n4EucZESCI4LZhQik306zD4VAuH2cb.  

Messages:
camrhG5tHzlY9WUSEVpVZGkU1tyJqKb5,s0OX2g7nYRctJxyFoQCa6clac9IsjHyi,
THIAtjllvYNlnTmiMnJEIHd2Ju4gqQIO,jwVk3JYZJNHloW7HO4LeGxFexknqro0v,
BFNRGOGmGGJNNPZqgeF1ikTNFfskbyLc,...

Were fixed in 4392.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4428 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-05 03:37:13 +00:00
ebanks aa00801108 remove reference to -mrl 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4423 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-04 17:27:01 +00:00
chartl f978c25b9d Perhaps both, Eric. Perhaps both. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4422 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-04 13:56:04 +00:00
chartl 0eb777612a Swap "." over to VCFConstants.MISSING_DEPTH_v3 
Why v3, you ask? Why not? Simply because v2 was a String so old and clunky, the sun would fizzle out and grow cold before any VCF could be successfully parsed.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4421 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-04 13:41:41 +00:00
chartl 74087c44ae Fixed a bug which caused a parsing exception when there was a variant with a dp field of ".", e.g. "GT:DP 0/1:." -- which can happen when using imputation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4420 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-04 12:37:36 +00:00
ebanks 6448753cf7 Removed the SequenomValidationConvertor and renamed it VariantValidationAssessor since it no longer handles ped/sequenom files (but instead works on vcfs/variantcontexts). Updated all of the wiki docs, including adding instructions on how to convert ped files to vcf, a la Shaun Purcell. We now officially no longer support ped files everyone. Other misc cleanup in the code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4419 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-04 02:11:38 +00:00
ebanks d8db48204e Fix typo and tell people not to post user errors 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4415 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-03 18:58:03 +00:00
ebanks 490e5e1b0f Better error when bad ref bases are provided 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4414 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-03 05:40:37 +00:00
aaron 64b7b3f83b fix for a recent change to the indexing code where we ignore the results of locking the file (this is bad), and as a result don't write the index; this should fix the build. 
Off to Yosemite in 4 hours, enjoy the week gsa folks!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4410 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-02 04:35:11 +00:00
depristo 7551ba8249 Trival refactoring in preparation for on-the-fly indexing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4409 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 22:32:59 +00:00
rpoplin 2f7892601c Useful debugging argument added to VariantRecalibrator to only use sites whose qual field is above --qual 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4406 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 21:08:55 +00:00
hanna 575c38fc04 Accidental fail to commit missing file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4405 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 20:26:51 +00:00
delangel d4398f2686 silly bug fix: if I'm to do a short term hack to avoid -infinity likelihoods I might as well do it right. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4403 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 18:39:45 +00:00
hanna 8d25a5f9f2 A mechanism for supplying attribution text -- mainly useful for external 
walkers.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4402 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 18:31:19 +00:00
delangel e920badcc4 Temporary fix for case where genotype likelihoods are exactly (1,0,0) or (0,1,0) etc. at a site with new indel genotyper: this would make us blow up when converting to log space and try to assign genotypes at a site. A more robust solution is in the works. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4401 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 17:43:43 +00:00
rpoplin b83fdf8a17 Bug fix in AnalyzeAnnotations. Be sure the site is a biallelic, unfiltered SNP. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4400 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 13:09:46 +00:00
delangel fa9c21c020 More fixes for exact AF calculation model in new unified genotyper: 
a) Fixed bugs in new dynamic programming-based genotyper
b) Fixed up temp hack that handles extended pileups for now.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4398 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 02:32:50 +00:00
delangel eb67aee732 bug fix: forgot to uncomment code to compute genotype likelihoods 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4397 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 21:38:22 +00:00
delangel ece694d0af Next iteration on new UG framework: 
- Brought over exact AF estimation from branch (which is now dead). Exact model is default in UnifiedGenotyperV2.
- Implemented completely new genotyping algorithm given best AF estimate using dynamic programming, which in theory should be better than both greedy search and any HWE-based genotyper.
- Integrated and added new Dindel likelihood estimation model.
- Corrected annotators that would call readBasePileup: since we can be annotating extended events, best way is to interrogate context for kind of pileup and either readBasePileup or readExtendedEventPileup.

All changes above except last one are still in playground since they require more testing.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4396 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 21:33:59 +00:00
hanna 4ea73bcfb1 Basic unit tests for WalkerManager. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4394 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 19:27:41 +00:00
hanna bf7fd08810 Fix newly-introduced bug in the PluginManager/DynamicClassResolutionException 
where, when the system can't find a plugin of the correct name, the system
prefers to crap all over itself and throw an unintelligible NullPointerException
rather than displaying an intelligent error.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4393 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 19:07:05 +00:00
hanna 14e19f4605 (Slightly) better exception text when SAM/BAM output file can't be created. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4392 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 18:43:22 +00:00
hanna 1fb8c86f6d Looks like we've got two competing models for an empty interval list: null and 
the empty list.  Score another victory for the integration tests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4391 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 17:11:47 +00:00
hanna 78343be52c At some time in the recent past, we lost our ability to process the '-L all' 
argument.  Brought it back, and added an integrationtest to make sure it
stays around.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 15:58:43 +00:00
delangel e80742e72f Use -o as argument for output file in ProduceBeagleInputWalker, to be consistent with other walkers (you're welcome, chartl :)). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4386 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 22:46:39 +00:00
hanna 732aa32758 Every Sting app from now on will be forced into the US English locale. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4385 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 21:55:21 +00:00
fromer 20ffe484bc Added detection and INFO field marking of phasing inconsistencies (and optional filtration using --filterInconsistentSites) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4384 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 19:28:56 +00:00
rpoplin a6c7de95c8 By using the AC info field instead of parsing the genotypes we cut 78% off the runtime of VariantRecalibrator. There is a new argument to force the parsing of genotypes if necessary. Various other optimizations throughout. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4383 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 18:56:50 +00:00
ebanks 2d1265771f Fix for G: make sure to generate the genotype conformations in the grid for the target frequency when not using grid search for anything except the conformations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4382 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 16:44:53 +00:00
delangel 4556e3b273 First iteration in filling up exact AF calculation with new refactored UG. Code computes EM iterations of exact AF spectrum and returns to caller. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4381 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 16:21:54 +00:00
ebanks 0d71dff928 Small bug fix to the new UG (need to initialize the entire posteriors array) means that we also get identical results as old UG when calling with 60 samples in the pilot1 data. Now that I'm happier with UGv2, I've transitioned it to use the correct AF priors instead of the busted ones still in the old UG. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4379 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 14:24:50 +00:00
hanna eee134baf2 Chris found a bug in the downsampler where, if the number of reads entering 
the pileup at the next alignment start is large, we don't add as many of those
incoming reads as we should.  No integration tests were affected.

Thanks, Chris!


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4378 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 11:18:12 +00:00
ebanks 0ec07ad99a Initial version of refactored Unified Genotyper. Using SNP genotype likelihoods and GRID_SEARCH AF estimation models, achieves the exact same results as original UG on 1-2 samples with the exception of strand bias (not implemented yet); other than that I have no idea. Needs tons more testing. Do not use. For Guillermo only. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4377 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 08:42:25 +00:00
kshakir 6df7f9318f For enums generate the full path to the Enum type to avoid collisions such as enum Model and enum Model used in the same class. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4376 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 05:28:59 +00:00
fromer e322e71c2f Restored SVN history for phasing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4373 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 00:02:02 +00:00
fromer 720aaca8a0 Trying to restore SVN history for phasing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4372 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 23:50:28 +00:00
fromer bf88117ead Trying to restore SVN history for phasing directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4371 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 23:48:24 +00:00
fromer dfb5143a41 Restore folder 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4370 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 23:46:07 +00:00
fromer 7c909bef82 Moved phasing classes out of playground! The code is still under production, though... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4369 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 23:21:28 +00:00
fromer 8d8980e8eb Fixed phasing algorithm to: 1. More correctly weed out irrelevant reads and sites; 2. Crudely flag sites with large phase discrepancies betweens reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4368 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 23:02:53 +00:00
chartl 5a5c72c80d Accidentally commited some debug output to PackageUtils, reverting change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4367 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 21:58:42 +00:00
chartl 862c94c8ce Small change for Matt -- output partition types in lexicographic order. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4365 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 20:08:03 +00:00
ebanks 7ad87d328d Make sure to uppercase ref bases since they aren't coming from the engine 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4364 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 19:05:46 +00:00
bthomas 96cccafb0d Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are: 
-- getToolkit().subContextFromSampleProperty(): filters a VariantContext to genotypes that come from samples that have a given property value
-- getToolkit().getSamplesWithProperty(): gets all samples with a given property
-- getToolkit().getSamplesFromVariantContext(): sample objects that are referenced by name in a VariantContext



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4361 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 02:16:25 +00:00
ebanks 1034853a84 Adding 'solexa' to list of known/supported platforms 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4357 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-27 02:38:38 +00:00
aaron 70f03a7113 first pass of well-formatted tribble exceptions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4352 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-25 03:29:33 +00:00
kshakir edaa278edd Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 
This will allow other programs like Queue to reuse the functionality.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4351 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-25 02:49:30 +00:00
hanna 497bcbcbb7 Recent changes to the build system make the build system complain loudly about 
pieces of core that depend on playground.  Most of these have been eliminated by
(temporarily) promoting Aaron's report system to core in this checkin.  I'll 
follow up with other changes in separately.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4350 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-24 22:09:12 +00:00
hanna 6ebca5d219 Enhancements to build external projects for walker sharing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4348 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-24 21:17:16 +00:00
corin eb1fa4bff3 changes an argument to an output so I can use it to track dependencies in queue 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4347 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-24 21:07:09 +00:00
depristo 745b8cc6d3 GATK now detects and UserExceptions when human lexicographically sorted data is provided 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4343 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-24 15:19:48 +00:00
rpoplin 1931b2e1bd Three fixes for VariantFiltrationWalker: Trying to filter an empty VCF file will produce a well-formed VCF file with zero records instead of a blank file, needed for pipelines. The first record's genotype info fields are now in the same order as all the others. The VCF header lines are pulled from just the input variant rod instead of from all rods. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4341 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-24 13:52:56 +00:00
kshakir 4ed9f437e9 Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts. 
The GAE half has all the walker specific code.  The new "Abstract" GAE has the rest of the logic.
More refactoring to come, with the end goal of having a tool that other java analysis programs (Queue, etc.) can use to read in genomic data.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4339 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-23 23:28:55 +00:00
rpoplin 0c9fabb06f Fix in AnalyzeAnnotations, somebody changed it look for ID in the vc's info field. This dinosaur desperately needs integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4338 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-23 19:48:44 +00:00
hanna 0c781968fb Tried to do a bit of pre-commit refactoring and screwed it up. Fixed. 
Thanks to Ryan for identifying the problem.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4336 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-23 18:17:29 +00:00
depristo d081b9b352 Improvements to error messages about @Requires and @Allows 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4334 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-23 12:08:27 +00:00
hanna 7841b301c4 Added more diagnostics so that I have some idea of what a 'general' exception 
is.  Required to fix bug ZjhCJAdwhtFq1x54ZlmlN8pFNcbrRpdJ and similar.  We
might want to change this particular case to a ReviewedStingException after
we gain a bit more experience with it.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4333 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 21:32:01 +00:00
fromer 44ccfc3531 Updated Phasing algorithm + evaluation module to properly implement haplotypes [including homozygous genotypes]; Implemented dynamic window phasing model for LARGE increase in efficiency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4332 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 21:29:58 +00:00
hanna 8f75d88519 Fix for GATK run report ids: 
mOVsxGfDiiSMxVs2PPTVjzYTVbizlD6e
  f9kUHUADFsZ0LiTGxRL5zPmq9kZcA4cQ
  8eGHWJFAlBVmgxwPi3sMd1RmiN2PwHOf
  iLhvHWveypKb2F8vKS5irHylc3pYvlOb
  HDttXKUMEVoPrvVeWrH7E0htxYyNydMx
plus a bit of cleanup of custom exceptions in the sharding system.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4330 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 19:49:25 +00:00
kshakir 20b38b38f3 Updated from SnakeYAML 1.6 to 1.7. 
Added a pipeline java bean and YAML utility to serialize java beans.
Added a getFirehosePipelineYaml.sh that can pull firehose data into the pipeline yaml file format.
Updated the fullCallingPipeline.q to begin using the pipeline yaml file format for bams and reference.
More changes to come as this code gets tested out in the fullCallingPipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4329 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 19:47:49 +00:00
hanna fb5d595ef0 Disable VCF header output in the Beagle integrationtest. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4327 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 16:50:03 +00:00
hanna 0c99c97685 The engine now automatically adds the command-line arguments to the header of every VCF, unless -NO_HEADER is specified. 
Changed integration tests, adding the -NO_HEADER argument, for walkers that previously did not include the command-line
arg headers.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4326 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 15:27:58 +00:00
aaron 1af9ca6d45 enabling tests that now pass with the conitg length validation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4325 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 22:20:50 +00:00
depristo 522830fb01 Support for --assume-single-sample in UG, better malformated bam exceptions, and ignoring out of order contigs in seqdictutils. All for the CG bam file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4323 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 20:33:34 +00:00
aaron 3938d53738 one broken build short of the hat trick. Fixing the unix test which expects the sequence dictionary of the Tribble track to equal the reference; we actually return the sequence dictionary of the track iself, with each contig set to the length of the sequence dictionary contig entry. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4322 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 18:47:20 +00:00
aaron b968af5db5 The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4321 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 18:21:22 +00:00
aaron 2586f0a1ca fix for the build I broke - the original file got corrupted, which I replaced with a version that didn't have the header stripped off. Other integration tests passed, but this test relied on the header being stripped off. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4320 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 15:35:25 +00:00
rpoplin 547763b230 Better error message for Petr's null pointer exception. Also added an exception integration test because I'm certain this used to work. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4319 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 13:44:40 +00:00
depristo 8719dde59d Now prints out PASS when a variant is unfiltered 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4318 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 13:16:41 +00:00