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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
hanna
ebanks
rpoplin
depristo
fromer
asivache
chartl
delangel
scalvo
kshakir
aaron