zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
4,655 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

3841 Commits (d492eb94ad2bb7e5c79a4d9cd051feca3abfd8a7)

Author SHA1 Message Date
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
delangel 205fc0b636 Cleanup: Use Tribble's version of createVariantContextWithPaddedAlleles (no real functional difference) to avoid duplicated code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4315 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-20 19:53:30 +00:00
delangel a10cfe213b Small bug fix in simple indel genotyper: Likelihood of case where best haplotype pair was (REF,REF) was not computed correctly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4314 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-20 17:04:39 +00:00
ebanks f5a30d0248 I just spoke to Andrey & Kiran (the original authors of these tools), and they voted to kill these in favor of Picard 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4313 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-20 13:27:35 +00:00
delangel f64b6fddc1 Major changes/improvements to indel genotyper: 
a) Redid way to compute path metrics in indel error model. Paper formulation where we have an anchor point in the alignemt between read and haplotype won't work in practice except in nice data sets that are perfectly indel-realigned and that are well mapped by aligner. New formulation doesn't assume this, and it's actually simpler and uses less code. It now resembles more a classic SW dynamic programming formulation but it still preserves the HMM probabilistic formulation. 
b) Added a programmable call threshold, set by command line.
c) Use now sample name from BAM file, remove -sampleName argument.
d) Simplify loop to compute read-haplotype likelihoods.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4311 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-19 23:47:31 +00:00
rpoplin c6351a11d6 Clearer logger output when not using by-hapmap 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4308 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-18 16:10:42 +00:00
rpoplin 7e58d8ed61 CombineVariants now outputs the command line in the VCF header. Added a new hidden argument to VR walkers called --NoByHapMapValidationStatus to turn off the by-hapmap dbsnp rod behavior. Very useful for experimenting with which sets to use as training data. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4307 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-18 16:06:50 +00:00
kshakir a3f31e5df0 When QScript writers use the RodBind, then the File version of the same argument should be optional, i.e. should not always try to output the file, which when unpopulated will be null. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4305 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 18:22:07 +00:00
bthomas c6c6d32b46 Quickly adding a new convenience method for retreiving a group of samples. The method is getSamples(Collection<String>) and returns a set of sample objects. There's also a test there. 
Ryan is using this to modify VCF code today...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4303 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 15:55:17 +00:00
kshakir a898908918 The output BAM file optional arguments of compression and whether to write an index are not outputs themselves. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4302 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 15:35:54 +00:00
bthomas bc12055fcf Quick patch to fix the sample code. It wasn't actually initializing the sample data source, so I added a call to initializeSampleDataSource() in GenomeAnalysisEngine. I think there was just an error resolving the versions of GenomeAnalysisEngine 
Also added a new error message that I thought would be helpful...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4301 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 14:05:26 +00:00
ebanks a10b2a00a5 Moving the util VariantContext 'modifying' routines into VC itself (as opposed to VCUtils) so that we can pass the genotype data directly into it and are no longer forced to decode the genotypes for no reason. This means that any walker that takes in a VCF and modifies the records without touching the genotypes never have to decode them. I've hooked this into the other two Variant Recalibrator walkers for Ryan. One side effect, though, is that we no longer can sort the sample names in the VCF (i.e. if the input VCF doesn't have samples in alphabetical order, then we used to sort them when writing a new VCF but no longer do that), because if we don't decode then we can't re-order the genotypes. I don't think this is a big concern given that the Unified Genotyper does emit sorted samples and that's the main source for most of the VCFs we use. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4300 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 07:09:58 +00:00
bthomas f66ef4626e Fixing two minor issues: 1) adding a new error message if the user adds a fasta file in a directory that doesn't exist; 2) renaming my sample unit tests so they actually run. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4299 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-16 20:45:51 +00:00
rpoplin 3a400e3dc0 Added CountCovariates integration test to ensure that it throws an exception if a variant mask isn't provided. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4298 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-16 19:18:38 +00:00
rpoplin 2eb5d9b2d2 CountCovariates makes sure that it sees a rod type that it expects for use as a variant mask (accepted types are dbsnp, vcf, and bed) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4296 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-16 18:53:42 +00:00
aaron de56568ce4 Adding the appropriate DbSNP file to the performance tests so they don't exception out. 
The exception: "org.broadinstitute.sting.utils.exceptions.UserException$CommandLineException: Invalid command line: This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation."


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4293 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-16 16:30:54 +00:00
aaron 782e0018e4 removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come. 
*** Three integration tests had to change: ***

RecalibarationWalkersIntegrationTest:
One of the tests was using the interval as the snp track, and wasn't supplying a DbSNP track (for CountCovariates)

SequenomValidationConverterIntegrationTest:
relies on Plink ROD which we've removed.  

PileupWalkerIntegrationTest: 
we no longer have implicit interval tracks, so there isn't a rod name over the specified region.  Otherwise the same result.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4292 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 22:54:49 +00:00
delangel c604ed9440 Several improvements to new indel genotyper (more to come soon): 
a) Turns out previous change of centering haplotype around indel was a bad idea. Context to the left of indel is important but not as important as right one, because by definition all alleles start at the same location, so haplotype is the same to the left of indel regardless of allele. So, go back to having a constant size window to the left of event.
b) Expand reference context so we can test larger haplotypes.
c) Optimize computation of read likelihoods by doing them in linear array instead of in a matrix - no difference in biallelic sites but could be significantly faster in multiallelic sites.
d) Bug fix: read alignment wasn't being computed correctly if, a) we were at an insertion, b) read started right at the insertion, c) read CIGAR didn't include insertion - more of these corner conditions are lurking, so a revamped computation of how reads align to candidate haplotypes is in the works.
e) Add debug option not to use prior haplotype likelihoods.
f) Don't hard-code NA12878 for genotyping, now sample name is a required input argument.
g) Bug fix: if there are no reads covering a candidate indel event, just output NO_CALL (didn't notice this in HiSeq, but in P1 data it happens all the time). I need to add a confidence threshold for calling later on.






git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4291 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 21:53:08 +00:00
depristo fb6d7d19f9 Better window size error message 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4290 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 20:40:56 +00:00
rpoplin b5d2e299d2 Make it more clear what is going on with the by-hapmap validation status in the dbSNP rod 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4289 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 17:29:31 +00:00
rpoplin 0a06fbdb94 Adding header lines to output of VR walkers to settle validator warnings. Command lines are added to the VCF header. GATK version numbers will be added to the header lines by Matt. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4288 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 16:45:03 +00:00
depristo 41fa323e63 Added iterator for tribble, fixing GS bug report. Removed unnecessary tabix double wrapping. Intergation tests to ensure the BTI works with both vcfs and vcf.gz 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4287 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 16:38:04 +00:00
asivache d7b5baf8e5 Now uses tagging of -I arguments. Multiple -I options (merging) is now allowed. In somatic mode 'tumor' and 'normal' tags are required for each input bam, the order does not matter anymore (since we use tags!) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4286 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 13:58:51 +00:00
bthomas e5f81d25d4 Adding the --sample-metadata (-SM) command line argument and associated functionality. This is something Matt and I have been working on for a while. Basically, it allows you to integrate sample metadata into an analysis, by including a sample file. More detailed documentation is on the wiki: http://www.broadinstitute.org/gsa/wiki/index.php/Adding_Sample_data_to_an_analysis 
This commit adds two important classes: Sample, which contains data about one sample; and SampleDataSource, which manages sample data a la ReferenceDataSource and ReadsDataSource. 

This code should be stable, but it has not been integrated with existing walkers yet. That's the next commit. 

In the meantime, feel free to experiment with the code - there are two basic example walkers in the playground.sample package. And PLEASE let me know if you see any errors/inconsistencies.

Note that this also adds a new dependency on SnakeYaml, a YAML parser.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4285 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 11:50:22 +00:00
ebanks dd23f204ab Making the UG args that allow users to proceed with insufficient bam headers (no SM or PL tags) @Hidden; removed them from wiki. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4283 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 01:54:50 +00:00
ebanks 514b28210e Have VF write to sdout when no -o is supplied 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4282 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 01:48:33 +00:00
ebanks 1901e3208e Oops, ran integration tests before Guillermo committed his change to the Beagle code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4281 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 01:41:02 +00:00
ebanks 4e83ba411f We now do lazy loading for the genotype data in VCF. Practically, almost all walkers end of loading the genotype data because we need to be smarter about transfering the unparsed genotype string when modifying VariantContexts; however, this does solve the problem for VR's piece to generate clusters (shaved off 75% of runtime for Ryan's large case). That further optimization will happen later. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4279 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 00:18:17 +00:00
depristo 74d4f124b1 Bug fixes to allow us to generate GATKRunReports for very early errors that leave the engine in a corrupt state. Vastly better error handling of common command line problems. Analysis output now notes whether an exception is a a UserException or a StingException 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4278 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 22:45:15 +00:00
delangel 2be5e862f1 forgot to commit change to MD5 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4277 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 19:28:03 +00:00
delangel 6d07181dc9 When processing Beagle output and creating new vcf, output the filtered records in the original input vcf as is, so that we don't lose the information on them when we run Beagle. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4276 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 19:18:45 +00:00
hanna 7fa6b2135b Added a back door so that integration tests can reset the sequence dictionary 
in the reference.  Reset routine is not accessible to any class outside
GenomeLocParser's package.

We'll have to do something more intelligent with this when the GATK goes
distributed.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4275 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 18:58:08 +00:00
depristo dbb641280e CycleCovariate now tolerates SOLEXA as machine type. Also, exception handling is now written to stderr. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4274 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 12:35:57 +00:00
ebanks 71d2d69b41 Better error message 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4273 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 05:04:26 +00:00
fromer 248cc308b2 ReadBackedPhasing silently ignores sites with ploidy != 2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4272 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-13 21:14:17 +00:00
fromer 528f6344af Moved ReadBackedPhasingWalker to phasing sub-directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4271 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-13 19:36:41 +00:00
depristo fa3be2209f Improvements to the error display code to print out the SVN number in all messages. Fixes to CallableLoci and tests to check for that case 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4270 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-13 18:36:45 +00:00
depristo 4d0ff336c2 Missed update input 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4269 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 15:46:13 +00:00
depristo 7880863eb7 Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4267 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 15:07:38 +00:00
depristo 7ad8fbdd5a Moved GATKException to exceptions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4266 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:47:19 +00:00
depristo 1876c9856a Moved stingexception 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4265 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:39:22 +00:00
depristo bccebf8899 Newly placed StingException 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4264 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:38:46 +00:00
depristo 3964e02fb6 Newly placed StingException 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4263 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:38:32 +00:00
depristo 595907e98e Moving StingException 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4262 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:34:15 +00:00
depristo 40e6179911 Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4258 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:02:43 +00:00
delangel da2e879bbc Miscellaneous improvements to indel genotyper: 
- Add a simple calculation model for Pr(R|H) that doesn't rely on Dindel's HMM model. MUCH faster, at a cost of slightly worse performance since we're more sensitive to bad reads coming from sequencing artifacts (add -simple to command line to activate).
- Add debug option to calculation model so that we can optionally output useful info on current read being evaluated. (add -debugout to commandline).
- Small performance improvement: instead of evaluating haplotype to the right of indel (just with a 5 base addition to the left), it seems better to center the indel and to add context evenly around event.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4257 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 13:50:28 +00:00
ebanks 61d511f601 Small memory performance improvement: remove the mapping from the hash instead of setting the value to null (i.e. remove the key too) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4256 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 05:19:09 +00:00
ebanks a0231f073f Damnit. Enabling the Picard code to recalculate all of the relevant SAMRecord attribute tags means that I need to have reference bases over all read bases even after realignment (and there are some big indels in dbsnp). Fortunately, I have my trusty IndexedFastaSequenceFile reader handy! Re-enabling the previously broken performance test. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4255 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 05:06:37 +00:00
hanna 87aca64716 Jumped the gun a bit on bam on-the-fly indexing -- Tim says it's not ready yet. 
Turned it off by default and added a property to turn it back on.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4254 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 21:16:03 +00:00
rpoplin 7b113a4886 Truncate the floating point numbers coming out of the variant recalibration walkers. Integration tests now work with both 1.6.0_16-b01 and 1.6.0_21-b06 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4253 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 18:37:49 +00:00
depristo 8f1a32acae All exceptions thrown by the GATK have been reviewed and UserErrors replaced where appropriate. Shazam. Another check-in will remove the GATKException and restore the StingException. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4252 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 15:25:30 +00:00
aaron cf33614ddc remove the test that's failing the performance tests, please don't release until this is figured out 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4251 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 06:30:40 +00:00
aaron 4adb07683d all fixed..thanks Matt! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4250 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 06:18:59 +00:00
aaron bd4bc84abd comment out the broken aligner test again - I'll take a crack at fixing it tomorrow. Each software engineer is going to take a pass at fixing it, and we'll see who can do it with the most style. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4249 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 05:22:24 +00:00
rpoplin 61e848c4f0 It's clear from Sendu's calling and my own calling that -qScale 100.0 is a much better default value for low pass data. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4248 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 01:47:21 +00:00
hanna e183b6598c - Fix our private repository of bwa reference support files. 
- Update the test to point to our repository.
- Update the md5 to reflect new Picard tag ordering.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4247 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 00:29:26 +00:00
depristo 1de713f354 Massive review of maybe 50% of the exceptions in the GATK. GATKException is a tmp. tracker so that I can tell which StingExceptions I've reviewed. Please don't use it. If you are working on new code and are considering throwing exceptions, it's either UserError or StingException, please 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4246 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 23:21:17 +00:00
kshakir 4183e8805a Fixed reference (via busted symlink) /broad/1KG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4245 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 20:34:51 +00:00
aaron f5c295b6b2 add a little bit of documentation to the RMD track builder and wrap any exceptions thrown in tribble with the file source and line that caused the error. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4243 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 17:56:36 +00:00
rpoplin aeb897db7f VR walkers look at by-hapmap validation status by default. Eric will be updating the syntax to allow for more flexibility here. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4242 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 15:40:56 +00:00
kshakir d7f55574e2 Re-enabling aligner integration test now that we're back to having more than 1 or 2GB memory. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4241 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 15:09:48 +00:00
rpoplin d625186796 I think the VR integration tests are fine. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4240 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 15:00:41 +00:00
depristo 6a30617a60 Initial implementation of UserError exceptions and error message overhaul. UserErrors and their subclasses UserError.MalFormedBam for example should be used when the GATK detects errors on part of the user. The output for errors is now much clearer and hopefully will reduce GS posts. Please start using UserError and its subclasses in your code. I've replace some, but not all, of the StingExceptions in the GATK with UserError where appropriate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4239 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 11:32:20 +00:00
depristo ca9c7389ee Not useful 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4238 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 02:33:03 +00:00
depristo 8708753a6a checkin for removal 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4237 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 02:32:46 +00:00
hanna 5119bdb55e - Update DoC to support output to /dev/null. 
- Add a release sanity check for DoC.
- Update release sanity checks with new command-line argument system.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4236 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 23:43:18 +00:00
fromer 1b1ec7e52d Changed default phasing window size to 10 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4235 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 21:28:36 +00:00
fromer ce031b2f05 PhasingEvaluator prints out interesting sites (only 1 phased, or phases disagree) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4233 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 18:21:21 +00:00
ebanks 40283f6456 Success! TranscriptToGenomicInfo now works without the delicate hacks that Ben had put in. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4232 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 18:06:00 +00:00
ebanks cd091d7309 This walker can NOT be tree-reducible (in its current state). Given that it's meant to be run just once for any given transcript set, this is not at all a problem. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4231 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 16:47:51 +00:00
ebanks ae9cba1c73 After an epic battle with this code until 3am last night, I have discovered that it is tragically and fatally busted. Ben clearly didn't understand how the ROD system works when writing it and so it is unusable in its current state. I've ripped out all code and it now gracefully exits telling the user that we are actively working on a replacement for this tool. Sigh. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4230 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 16:39:41 +00:00
ebanks 29f7b1e6d6 Trivial update 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4229 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 14:02:38 +00:00
ebanks cd2bfb09ef Change for Tim: invalidate the MD tag (temporarily) if it exists in a read that gets realigned 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4228 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 13:59:09 +00:00
ebanks 65edbced36 Addition for Tim: recalculate the NM and UQ tags after realignment. Also, don't fix the insert size calculation, since that's done by fix mate information. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4227 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 04:02:14 +00:00
chartl 71046e650e Added a more robust check for Jishu -- am pretty sure the .bam header is busticated 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4223 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 01:11:22 +00:00
fromer ae3f7026a4 Corrected phasing quality evaluation to correctly account for hom sites that break phase 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4222 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-07 22:43:54 +00:00
hanna 501f6a0e14 Temporary hack to disable index creation when target BAM is /dev/null. Tim 
promises me that Picard will put in a real solution next week.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4220 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-07 16:57:51 +00:00
fromer 754c2c761e Added minimum phasing quality for phasing evaluation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4219 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-07 14:29:11 +00:00
ebanks 5d0d9c7dce My parallel version of TranscriptToInfo now emits 'chr start end' instead of 'chr:start-end' for records so that 1) they can be easily sorted in coordinate order (allowing me to emit records out of order if I choose) and 2) the file can be tabix indexed (when we stop finding 'critical' bugs in that code). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4218 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-07 05:20:40 +00:00
ebanks 4d4ef5b42c In the end, it's not worth rewriting TranscriptToInfo from scratch. I'm keeping the old one around for a bit so I can play with this new version which 1. doesn't store the records in memory so can be run in under 1Gb of memory, 2. actually emits all of the records (the original fails in some cases), and 3. is refactored to cut out ~20% of the code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4215 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-06 02:37:34 +00:00
kiran 0dd5a0990d Now annotates sites marked as filtered out (this is important if sites are in a lower-quality tranche). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4214 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-04 00:36:55 +00:00