8c583ea405
RBP now operates correctly at non-variant sites so we can phase hom-ref genotypes with -sampleToPhase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4903 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-23 13:11:22 +00:00
376bc563d4
Trivial change to allow GenerateVariantClusters to be run on indels - not that VQSR now works on indels, far from it, but at least it's a first step and it allows us to generate cluster plots to see how well known/novel sites differentiate in their covariates (short answer: no difference/separation :( ).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4902 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 22:39:09 +00:00
e313eeede8
Push command-line expansions, such as BAM list unpacking and -B tag parsing, out
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into the CommandLine* classes. This makes it easier for external functionality
(such as the VCF streamer) to use GenomeAnalysisEngine directly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4897 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 19:00:17 +00:00
66cca7de0f
renamed genotypesArePhased to isPhased, as the previous name was incorrect for several reasons. Added setPhase() to MutableGenotype. Other classes changed to reflect renaming to isPhased(). CombineVariants now supports an experimental MASTER mode where it consumes -B:master,vcf and -B:xi,vcf for any number i and updates the master with phasing information in xi.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4896 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 17:42:05 +00:00
2235245af0
PrivatePermutations generalized to compute transition counts and average probabilities (and thus was renamed). Changes in some pipelines to reflect the change. Bugfix in the batch merging pipeline (it would halt because the allele VCF for genotyping batches could become off-spec).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4894 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 15:16:15 +00:00
a1653f0c83
Another major redo for indel genotyper: this time, add ability to do allele and variant discovery, and don't rely necessarily on external vcf's to provide candidate variants and alleles (e.g. by using IndelGenotyperV2). This has two major advantages: speed, and more fine-grained control of discovery process. Code is still under test and analysis but this version should be hopefully stable.
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Ability to genotype candidate variants from input vcf is retained and can be turned on by command line argument but is disabled by default.
Code, by default, will build a consensus of the most common indel event at a pileup. If that consensus allele has a count bigger than N (=5 by default), we proceed to genotype by computing probabilistic realigmment, AF distribution etc. and possibly emmiting a call.
Needed for this, also added ability to build haplotypes from list of alleles instead of from a variant context.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4893 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 02:38:06 +00:00
09c7ea879d
Merging GenomeAnalysisEngine and AbstractGenomeAnalysisEngine back together.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4889 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 02:09:46 +00:00
b3ac47812c
No longer emits records at filtered sites, in sub-sampling mode
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4883 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:43:50 +00:00
60880b925f
VC utils prune method now will keep genotype attributes as well as info keys. RBP now emits a far reduce (NO INFO, only GT:GQ:PG) records, further reducing size of phasing output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4882 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:33:14 +00:00
8604335566
Minor improvements to further reduce debugging output. When running in -samplesToPhase mode, now only including the samples to phase in the output VCF, making it very much smaller.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4881 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:19:47 +00:00
ff90c24f28
RBP now supports operating on a subset of samples, outputting a much reduced VCF file appropriate for merging later. Also, general optimization to avoid printing enormous amounts of data to logger.debug by using a glocal static variable DEBUG that conditionally allows writing to the variable. Passes integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4880 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:03:28 +00:00
a3729bd59c
Now I call BeforeMethod correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4872 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 22:45:45 +00:00
b7e4a015c0
static thread cache reset in UnitTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4870 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 21:53:10 +00:00
3bbc6a0540
Slightly more thread safe CachingIndexedFastaSequenceFile.java. Likely passes parallel testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4869 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 21:05:17 +00:00
5dd0e8388b
Fixed a bug in UnitTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4867 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 19:44:35 +00:00
4a54f3f230
ThreadLocal version of CachingIndexedFastaSequenceFile. More efficient support for shared memory BAQ calculations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4865 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 15:44:48 +00:00
32d5397c01
Experimental support for sided annotations. Currently not more/less valuable than two-tailed testing. Future experiments are needed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4864 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 15:08:31 +00:00
21dc05138a
Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4863 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 14:49:15 +00:00
2bd2667516
Another privately-owned class to add before re-checking out repository
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4858 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 18:14:51 +00:00
e406eb0f95
Adding a useful accessor method to TableFeature
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4856 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 18:11:51 +00:00
8ab4704b4c
Adding a command-line argument to allow missing values to evaluate as false instead of true
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4854 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 05:18:12 +00:00
9f3e56e487
VariantAnnotator shouldn't die when multiple records occur at the same position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4853 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 04:05:47 +00:00
acfe83920b
'-L unmapped': adding integration tests for explicitly including (-L unmapped)
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unmapped reads and explicitly excluding (-XL unmapped) unmapped reads, augmenting
the suite of unit tests already put in place.
'-L unmapped' seems safe to use; go for it, but please validate results against
samtools flagstat when the process finishes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4849 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 23:11:46 +00:00
dabdeb729e
Eric broke the build. Eric broke the build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4847 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 17:01:38 +00:00
5c0b66cb7c
3 big changes that all kill the integration tests: 1. Don't cap the PLs by 255 anymore. 2. Move over to the 3state model as the only available base model for UG (no more base transition tables). 3. New QD implementation when GLs/PLs are available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4846 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 16:24:28 +00:00
5a27d231fa
Rename it so that nobody else falls into the trap laid out (the test is VariantToTable, the walker is Variant[s]ToTable)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4844 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 11:43:00 +00:00
5e27e9162f
Huh? I thought we parsed out comma-separated command line arguments into list automatically...just change the syntax of the integration test, no need to update the md5
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4843 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 11:40:27 +00:00
3e75431bc8
Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4842 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 03:33:36 +00:00
01323447c6
Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM.
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Fixed integration tests to wait on their own for the job to run instead of using SUB2_BSUB_BLOCK.
Updated VariantRecalibrationIntegrationTests MD5s which were knocked out of sync whele SUB2_BSUB_BLOCK was exiting in the middle of integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4840 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 19:57:20 +00:00
67c07d1a6a
Fixed recently introduced multiplexer issue where DoC couldn't be written
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directly to command-line.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4839 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 19:35:15 +00:00
526ae92093
Getting back to '-L unmapped':
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- basic unit tests for interval sorting and merging with mix of mapped/unmapped.
- validation to ensure that locus walkers (really all non-read walkers) blow up with a user error when -L unmapped is specified.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4837 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 18:24:18 +00:00
afd4655674
Use @Output instead of @Argument. As a side note, Chris I'm ready for this nightmare to go away...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4835 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 17:13:15 +00:00
cf7d932a17
Fix for f***ed up BWA alignments that adhere to SAM specs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4834 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 17:12:25 +00:00
d550fdfd60
Disabling integration test to see if this restores the full test suite.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4833 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 15:27:02 +00:00
a5008faca8
Bug fix: when getting variant contexts at a site, we need to get only variants that start at current location, otherwise we get duplicated records when filtering indels.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4830 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 19:23:10 +00:00
17db2e0e24
(forgot I hadn't committed this) - refactored IndelStatistics module and added a new inner class to compute Indel classification along with other statistics. So, we now get an extra table specifying, per sample, counts of whether indels are:
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- Repeat Expansions
- Novel sequence
And for indels of size <=2 we get a per-mononuc. or dinuc. breakdown of novels and expansions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4828 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 17:43:43 +00:00
cf75caf653
java changes:
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VariantEvalWalker's logger is made public, so that variant eval modules can access it through the parent object.
DesignFileGenerator comment lists how best to bind things to it, and the feature accessor is better refined to grab the genome loc. (old change)
scala changes:
convenience addAll( List[CommandLineFunction] ) added to QScript class (and thus removed from the fCPV2)
useful command line functions added to a new library package for command line functions (these are fast simple VCF command lines)
bug fixed in ProjectManagement for the class where there's only one batch to be batch-merged (not really part of the use-case, but an edge-condition that came up during pipeline testing)
first draft of a private mutations pipeline which will be elaborated in future
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4823 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-12 05:10:45 +00:00
abd6ce1c77
A TiTv-free approach for cutting variants! Apparently much better than previous approach, and will work for indels and SV will truly minor modifications to the code. Will discuss with methods group on Monday.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4822 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-11 23:08:13 +00:00
974aaa134d
Trival fix to broken build
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4820 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-11 13:56:03 +00:00
895cb39f41
Thanks to Platform Computing tech support, found the magical environment variable BSUB_QUIET.
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Minor refactoring to add more of the CLibrary including setenv().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4819 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 21:27:12 +00:00
5b46a900b3
Final version of BAQ calculation. default gap open is 1e-4, a good sensitive value. Useful timer class SimpleTimer added. BAQ is now live.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4818 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 19:35:12 +00:00
491a599b59
Minor optimization
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4817 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 18:56:35 +00:00
56433ebf6b
Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects:
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- bsub command line is no longer fully printed out.
- extraBsubArgs hack is now a callback function updateJobRun.
Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q.
Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits.
Updated VE packages that live in oneoffs to compile to oneoffs.
Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4816 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 04:36:06 +00:00
d4d3170436
Support for '-L unmapped' in read walkers. DO NOT USE THIS PATCH YET. It has been
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subjected to and passes cursory testing on one dataset (and all integration tests pass).
However, there's a small library of validation checks, and unit and integration tests
that must be added.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4813 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-09 19:51:48 +00:00
a2d6cef181
Weird corner condition fix in indel genotyper: if there are 2 consecutive locations on candidate sites to genotype, we can get both when calling getVariantContexts and if we are triggering on an extended event - this leads to confusion and we can end up picking the wrong one. So, we require start of the vc to be the same as the start of the ref locus to be sure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4812 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-09 19:34:23 +00:00
722819688a
Minor utility improvements to ValidateBAQ
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4809 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-09 02:19:32 +00:00
a63bbb2fec
Optimized BAQ implementation. No longer does excessive amounts of copying of arrays. At this point I'm not 100% certain where additional performance improvements would come from
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4808 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-08 21:26:30 +00:00
db55b2b0c6
Better testing of BAQ. Now really handles soft clipped reads properly by doing an expensive copy operation :-( will need to be transformed to a ByteBuffer in the near future.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4807 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-08 17:37:00 +00:00
f1f01610f8
Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4806 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-08 17:22:29 +00:00
16e1bbd380
Hidden command line option to control BAQ gap open penalty for testing by me and eric. ValidateBAQWalker has misc. useful improvements. PrintReads now adds BAQ tags on output, if requested.
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BAQ has generally useful improvements. Refactor code to make it easier for BAQUnitTest to run. minBaseQuality enforced on output, as well as input now. Added BAQUnitTest that checks that the BAQ calculation is performing as expected. Still needs to be expanded significantly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4804 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-08 01:01:39 +00:00
1b6bec8e6b
Trivial changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4803 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-07 20:06:54 +00:00
ca7810f11d
First major update of indel genotyper:
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a) Really fix this time strand bias computation for indels, previous version was a partial fix only.
b) Change way in which we deal with bad bases at the edge of reads. Even if a base is soft clipped in CIGAR string, there may still be dangling bases with Q=2 that may throw off QUAL computation in some sites. So, we're stricter and we also trim off those bases off read edges even if they are not soft-clipped officially.
c) First feeble-minded attempt at runtime optimization - don't compute log and 10^base_qual every time. Rather, cache 10^-k/10 and log(1-10^-k/10) for all k <=60. This speeds up code about 4x.
d) Further optimization: don't compute log(10^x+10^y) but rather use softMax function recently put into ExactAFCalculationModel.
e) Skip bad reads where all Q=2 (sic)
f) Avoid log to lin and back to log conversions of genotype likelihoods - this was legacy code from back when exact model did stuff in linear domain. This improves precision overall.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4802 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-07 18:35:22 +00:00
e2d45ec2af
Make Indel Realigner exceptions related to not enough space on disk or a too low file-handle limit UserExceptions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4801 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-07 16:37:31 +00:00
70980b659a
CombineVariants no longer requires rod_priority_string
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4800 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-07 15:39:43 +00:00
bc885b7bd0
Don't print debugging output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4799 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-06 20:57:11 +00:00
c91712bd59
BAQ calculation refactoring in the GATK. Single -baq argument can be NONE, CALCULATE_AS_NECESSARY, and RECALCULATE. Walkers can control bia the @BAQMode annotation how the BAQ calculation is applied. Can either be as a tag, by overwriting the qualities scores, or by only returning the baq-capped qualities scores. Additionally, walkers can be set up to have the BAQ applied to the incoming reads (ON_INPUT, the default), to output reads (ON_OUTPUT), or HANDLED_BY_WALKER, which means that calling into the BAQ system is the responsibility of the individual walker.
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SAMFileWriterStub now supports BAQ writing as an internal feature. Several walkers have the @BAQMode applied to this, with parameters that I think are reasonable. Please look if you own these walkers, though
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4798 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-06 20:55:52 +00:00
5d2c2bd280
Just refactoring into utils/baq directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4795 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-06 17:43:43 +00:00
80f32712dc
Tiny bug fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4793 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 18:48:33 +00:00
44feb4a362
Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4792 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 18:29:39 +00:00
8901e63879
Cheap optimization: don't keep calculating the log of a constant. (How did I not catch this before?)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4791 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 04:36:21 +00:00
bef48e7a42
For Chris, to make his life easier: iterate over all VCF records passed in looking for one with an ALT allele defined instead of assuming all records have one.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4789 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 02:23:38 +00:00
97c94176c0
Immediate, obvious bug fix to avoid blowing up on unmapped reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4788 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-04 20:43:39 +00:00
a5b3aac864
Engine-level BAQ calculation now available in the GATK [totally experimental right now]. -baq argument to disable (NONE), to only use the tags in the BAM (USE_TAG_ONLY), use the tag when present but calculate on the fly as necessary (CALCULATE_AS_NECESSARY), and to always recalculate (RECALCULATE_ALWAYS). BAQ.java contains the complete implementation, for those interested. ValidateBAQWalker is a useful QC tool for verifying the BAQ is correct. BAQSamIterator applies BAQ to reads, as needed, in the engine. Let me know if you encounter any problems. Before prime-time, needs a caching implementation of IndexedFastaReader to avoid loading *lots* of reference data all of the time
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4787 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-04 20:23:06 +00:00
b12cec4302
Added emitOnlyMNPs flag
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4785 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 20:34:17 +00:00
6d4ec7f9e7
Remove RefSeq INFO from MNPs since annotating them properly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4784 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 19:03:35 +00:00
4719bbc772
Changed dontRequireSomeSampleHasDoubleAltAllele parameter to mean that merging should only start at a polymorphic site
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4783 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 17:52:56 +00:00
ec174dc0ba
As per Menachem's last commit, there's a minimally more efficient way of doing the MQ cap.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4782 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 16:37:08 +00:00
92cf7744a6
Set minMQ = max(minMQ, minBQ) for phasing since anyway we cap BQ by MQ; also, lowered MIN_BASE_QUALITY_SCORE for phasing to 17 (was previously 20)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4781 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 16:31:13 +00:00
237ab1d489
1. As discussed in group meeting today, because we cap BQ by MQ, if MQ < minBQ then we filter the read.
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2. Update to UGCalcLikelihoods for Chris: require a vcf bound to 'allele' to be provided so that we know exactly which alternate allele we should be calculating GLs for at each site. The user is warned when the VC is not biallelic or there are multiple records at a site.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4780 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 05:57:06 +00:00
da6a07ad3b
First round of critical fixes to indel genotyper (more to come tomorrow):
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a) Avoid complete crash of caller that broke due to a recent refactoring by someone who must not be named <cough>EB<cough>... an integration test to avoid this in the future coming soon.
b) Fixed up strand bias computation for indels
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4779 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 02:48:09 +00:00
e09d6ee56b
write non-MNP VariantContexts records only once (where they start)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4777 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 22:14:26 +00:00
1515bf6de9
Merged common VCF writing logic into phasing/WriteVCF.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4776 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 22:03:02 +00:00
4e62de4213
Added method getOriginalReadGroupId(): takes merged (in case of collision) read group id as reported by a read coming from the merged stream and returns this read's read group id as it was listed in the original input bam file.
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IndelRealigner now uses this functionality to correctly un-mangle read group id's in --nWayOut mode (i.e. when we need to write reads into separate output bams with headers matching the original inputs).
Some hidden changes to IndelRealigner: purely testing and development, transparent to the users (hidden option added)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4775 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 21:41:52 +00:00
e5282742f9
Bug fix in CountCovariates, skip over indel records as well as SNPs in the dbsnp file. CountCovariates is now called CountCovariatesWalker. I've always hated that the name was swapped.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4774 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 18:43:24 +00:00
0adf505b53
We no longer look at by-hapmap validation status in the VQSR because using the HapMap VCF file is higher quality. As a side effect we now support the dbsnp 132 vcf file. ApplyVariantCuts now requires that the input VCF rod bindings begin with input, matching the other VQSR walkers. Wiki updated with information about how to obtain the hapmap and 1kg truth sets.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4772 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 15:38:45 +00:00
99b942b0b4
Removing duplicated header args
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4770 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 20:16:53 +00:00
9ac0f98d0d
Fixed bug in retaining proper RefSeq records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4768 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 18:39:02 +00:00
7caf666f48
For Sendu: add a hidden option to allow bams to come out unsorted. We've agreed to let him deal with sorting these puppies on his own.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4767 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:56:13 +00:00
3afa841a6a
Fixing docs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4766 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:36:47 +00:00
6a6cdc1925
Adding minor usage docs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4765 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:34:33 +00:00
0d1c905df3
Adding UGCalcLikelihoods and UGCallVariants so that GSA members can break up the calling process into separate steps (calculate the GLs and then call off of those) - useful for Chris's new batch merger. As the docs say, these are absolutely not supported or recommended for public use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4764 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:32:26 +00:00
b4ef716aaf
As per Eric and Mark's suggestions, separated the segregating MNP merger (MergeMNPs) from the more general merger employed for annotation purposes (MergeSegregatingAlternateAlleles). Both use the same core MergePhasedSegregatingAlternateAllelesVCFWriter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4763 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 16:42:08 +00:00
0892daddb0
Improvement for the TGEN folks: when running in the solid recal mode of SET_Q_ZERO_BASE_N, update the NM tag if one was present in the read to reflect the new N's in the read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4761 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 04:36:44 +00:00
a22b1b04e6
SW-turbo. Kind of. This implementation is presumably equivalent to the old one (mathematically), but runs ~10 times faster: inner loops eliminated completely. The author of the original implementation should be sentenced to the galleys. Oh, that would be me...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4760 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 00:08:47 +00:00
2ac938fe4e
1)
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Minor fixes to avoid crashes vs CG indel files:
- Add count for complex events, not just insertions and deletions
- Handle correctly cases of large indels falling out of bounds of histogram array: added a count of indels ouf of bounds and avoid exceptions.
2) Cosmetic fix for R script assessing UG calling performance: draw red y=x line on top of Simulated vs Estimated AC to get a better view of under/over-estimation of AC.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4758 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 21:08:25 +00:00
af84462f3e
The dev team has decided to change the filter that is added to records that are set to monomorphic by Beagle. It no longer lists the reference allele. Added those filters to the header of the output VCF file. Finally, we no longer use R2=NaN values coming from Beagle.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4757 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 17:19:54 +00:00
21256909bb
Not supported. I'm checking this in for Ryan only.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4756 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 16:59:18 +00:00
e21a66d876
Updated the Queue GATK generator and packaging to include more dependencies for fullCallingPipeline.q.
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Set the -bigMemQueue in the FullCallingPipelineTest to GSA to avoid waiting for the week queue when it is busy.
Fixed the package definition of PipelineTest so that scalac won't recompile it every time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4755 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 15:29:40 +00:00
7f2ded0706
belated special case fix for Menachem; if the results of a BTI and BTIMR produce an empty interval list, exception out. This would be solved long term with better handling or empty and / or null interval lists. I'll add a JIRA
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4754 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 05:49:20 +00:00
a181680814
We no longer require dbSNP files to be of the dbsnp rod-type; VCFs will do (provided they are bound to the name 'dbsnp')
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4753 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 03:25:18 +00:00
8ffea42b75
about 10% improvement in SW alignment (and hence IndelRealigner!) speed by using c-style linearized array representation for matrices instead of java 2D arrays...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4751 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 00:06:50 +00:00
b03ac61e9d
consolidating the checking of the RMD sequence dictionary against the reference into a single function, and adding an integration test to test that empty VCFs pass (both the indexing and the seq dictionary validation).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4750 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 00:01:56 +00:00
abc13d0a90
Temporary hack: force abort with an intelligent message suggesting that users
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specify -B:dbsnp,vcf <filename> if the filename passed if the --DBSNP argument
value contains 'vcf'. We'll replace this functionality once dbSNP 132 starts
playing nicely with the tagging system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4749 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 23:37:30 +00:00
d89e17ec8c
Fare thee well, UGv1. Here come the days UGv2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4747 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 21:51:19 +00:00
727dac7b7a
Added MNP annotation of the number of AA changes occuring in the SAME RefSeq entry (numAAchanges), and if this number is > 1 for any of the alt alleles (alleleHasMultAAchanges)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4746 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 21:24:30 +00:00
222cd42ceb
Have the UG engine take care of the GL to PL conversion. Note that we still use GLs for calling (since we are losing precision in high-pass and, even worse, it can affect QD), but we emit PLs in all cases. This means that calculating the GLs, emitting them to VCF, and then calling off of them (a la samtools) is absolutely, positively not ideal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4745 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 20:28:16 +00:00
102c8b1f59
Large refactoring of the UGv2 engine so that it is now truly separated into 2 distict phases: GL calculation and AF calculation, where each can be done independently. This is not yet enabled in UGv2 itself though because I need to work out one last issue or two. Tested on 1Mb of 1000G Aug allPops low-pass and results are identical as before. Also, making BQ capping by MQ mandatory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4744 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-28 21:36:33 +00:00
ce051e4e9a
Write to sdout when no -o is provided
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4743 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-28 06:19:26 +00:00
e3e6d176df
Looking over the daily error log email made me realize that there were 2 implementations of vc.modifyLocation() - the correct one in VC that didn't require lazy loading the genotype data and the bad one in VCUtils that did. Removing the implementation in VCUtils and updating the code accordingly. Also, removing createPotentiallyInvalidGenomeLoc() since no one uses it anymore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4736 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-26 18:40:34 +00:00
35b90d2295
Don't compute SB for ref calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4735 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-26 03:54:26 +00:00
6934f83cc7
Two changes to CombineVariants.
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1. Fix: VCs were padded before the merge, but they were never unpadded afterwards. This leaves us with a VC that doesn't meet our spec.
2. Update: instead of running the merged VC through every standard annotation (which seems really wrong, since this isn't the annotator tool), just update the chromosome count annotations (AC,AF,AN) through VCUtils.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4734 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-25 04:52:12 +00:00
d775192631
Check if MNP annotation of amino acid is dependent on the MNP, or could it be obtained through some single-base variant?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4733 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 22:38:33 +00:00
0dd40c3684
Updating doc text
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4732 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 21:34:14 +00:00
ed08899abc
Overwhelming evidence that maxQ = 50 is now a better default than maxQ = 40 in the base quality score recalibrator, especially when combined with dbsnp build 132. Also, added option in ProduceBeagleInputWalker for Beagle-ing chromosome X calls with male samples which sets the genotype likelihood for the AB allele to zero for those samples.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4731 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 21:32:26 +00:00
ca70ed611c
Totally revamped the MNP annotation and put it in its own walker: AnnotateMNPsWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4730 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 18:05:10 +00:00
8768e1a240
Useful profiling tool that reads in a single rod and evalutes the time it takes to read the file by byte, by line, into pieces, just the sites of the vcf, and finally the full vcf. Emits a useful table for plotting with the associated R script that can be run like Rscript R/analyzeRodProfile.R table.txt table.pdf titleString
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4728 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 14:59:16 +00:00
7a8b85dd15
Catch the JEXL exception when trying to match a variable that's not in the context - and don't filter in these cases. Now everyone can happily go back to using the stupid (and hopefully temporary) AlleleBalance filter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4727 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 05:00:41 +00:00
caf2c21f61
Must close the writer to flush the cache
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4726 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 04:33:08 +00:00
816c33c821
indel-related fixes to the strict validator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4725 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 04:08:34 +00:00
9cdc341be5
Trivial update for data processing paper: change syntax of output argument for Beagle by depth walker to update to new GATK format.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4724 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 01:45:44 +00:00
ea6e2218c1
1. dbsnp has some massive indels which my left-aligner was barfing on because there isn't enough reference context; fixed. 2. Lower default calling threshold to Q30 for UGv2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4722 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 19:28:33 +00:00
53672361cc
capture more details when something IO-related goes wrong in writing a Tribble index
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4720 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 17:06:28 +00:00
082073ca3c
Stop RBP.getPileupBySample() from throwing a NullPointerException if the
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sample doesn't exist -- now returns null.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4719 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 05:17:06 +00:00
787e5d85e9
Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.
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Added an initial test for genotyping chr20 on ten 1000G bams.
Since tribble needs logging support too, for now setting the logging level and appending the console logger to the root logger, not just to "org.broadinstitute.sting".
Updated IntervalUtilsUnitTest to output to a temp directory and not the SVN controlled testdata directory.
Added refseq tables and dbsnps to validation data in BaseTest.
Now waiting up to two minutes for gather parts to propagate over NFS before attempting to merge the files.
Setting scatter/gather directories relative to the -run directory instead of the current directory that queue is running.
Fixed a bug where escaping test expressions didn't handle delimiters at the beginning or end of the String.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4717 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-22 22:59:42 +00:00
8ca5edf89f
Fix issue where non-required file inputs can throw a NullPointerException
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rather than a UserException when an the input argument is specified without
an argument value.
The magnitude of code required to fix this points to a need to give the
command-line argument system a good spring cleaning.
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2010-11-22 01:49:17 +00:00
b9a59ea54f
Adding Het/Hom ratio to the temp per sample metrics. Because I'm in a generous mood tonight, I'm going ahead and fixing the paths for the classes I'm touching...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4713 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-21 04:24:42 +00:00
cff7c6ddce
These are user exceptions
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2010-11-21 02:08:11 +00:00
374c0deba2
Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4711 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-19 19:59:05 +00:00
c723db1f4b
Added a -summary jexl argument to VariantEval similar to -validate.
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Updated the package of ValidationGenotyper to match the file location.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4710 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-19 04:42:46 +00:00
79725f2d9c
Excluding the QFunction log files from the set of files to delete on completion.
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When a QGraph is empty displaying a warning instead of crashing with an JGraph internal assertion error.
Cleaned up code using the Log4J root logger and explicitly talking to a logger for Sting.
When integration tests are run detecting that the logger has already been setup so that messages aren't logged twice.
Updated from Ivy 2.2.0-rc1 to 2.2.0.
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2010-11-18 20:22:01 +00:00
721e8cb679
VariantsToTable now supports wildcard captures. -F PREFIX* now captures all fields that begin with PREFIX, output as a comma-separated list of unique values. Added integration test for VariantsToTable since I find it so useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4706 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 18:54:59 +00:00
8cba86a69d
Trivial code organization for the haplotype score
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4703 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 12:32:55 +00:00
9f356b6cd0
Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4702 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 02:33:45 +00:00
90711d445c
Change the interface for RMDTrackBuilder, therefore always mandating the specification
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of a sequence dictionary and related info. This will hopefully eliminate the cases in
which the refseq track depends a sequence dictionary / contig parser that hasn't been
specified.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4700 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 19:00:17 +00:00
367cc9135f
Use VariantContext and Genotype accessor methods for attributes that will return null for unparseable data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4699 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 18:19:56 +00:00
2f3578182a
Added VERY preliminary version for merging refseq annotations as SNPs are merged
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4698 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:49:12 +00:00
e2f7f33ce7
Added getIntegerAttribute()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4697 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:33:07 +00:00
d86ab2becb
JEXL expressions now generate exceptions, not warnings. Tools should catch the runtime exception to handle correctly. Removed unncessary complexity from the JEXL contexts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4695 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:08:16 +00:00
539651de30
Initial version of Indel Statistics module for Variant Eval - not for general use yet, needs more verification and more work. Older IndelHistogram module will be obsolete with this new walker. Right now, for each sample (and for all samples), the following are computed:
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- Number of insertions
- Number of deletions
- Length distribution for indels.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4694 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 15:52:01 +00:00
01b721ab61
Passing ReviewedStingExceptions through the HMS.
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Added a @Hidden experimental argument -validate to VariantEval that allows external JEXL assertions that must evaluate to true will throw an exception.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4692 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 21:50:42 +00:00
24ec35deaf
- Reintroduce test dependency so that the tests passing / failing is not
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dependent on the contents of the integrationtest directory. Will figure
out how to better manage the integrationtest directory at some point in
the future.
- Up the max heap size for tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4691 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 19:55:20 +00:00
62f02bf30a
Minor JAVA visibility updates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4690 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 15:28:58 +00:00
f1b0f3bc49
Putting my changes from earlier in the day back in after someone (rhymes with 'Dark') trounced on them with his last commit...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4687 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 01:55:50 +00:00
8ff4e4cb25
Cleanup testng listener configuration.
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- Add StingTextReporter, which provides a text dump of the errors to the
console. Had to create our own reporter (inheriting from the standard
TestNG TextReporter) to work around a configuration issue with the
TextReporter. In an ideal world, I'd report this on the TestNG mailing
list and help them resolve the issue, but this solution is relatively
robust at the moment and life is too short.
- Added back the failed test listener, which generates the testng-failed.xml
file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4686 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 23:43:14 +00:00
b677080858
Initial checkin of the ValidationGenotyper. Not intended to be used by anybody yet. Only here for archival purposes at this point.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4685 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 22:33:49 +00:00
ef2f6d90d2
VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4684 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 22:19:22 +00:00
5b83942cee
- Fix DepthOfCoverage so that, when it abuses the ROD system by instantiating a track in onTraversalDone, it also supplies the correct sequence dictionary and parser.
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- Changed RMDTrackBuilder to use SequenceDictionaryUtils.validateDictionaries for ref <-> ROD sequence dictionary validation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4683 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 20:34:04 +00:00
2af508ef83
Better docs, as requested by Matt
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4681 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 18:24:15 +00:00
62be55376b
no longer useful
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4677 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 17:53:33 +00:00
35382468ee
Better error checking/output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4676 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 16:36:34 +00:00
7a3a464959
Finally, the logic is right
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4674 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 14:02:09 +00:00
8d66637fc2
Bug fix for VariantsToTable with filtered records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4673 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 13:49:16 +00:00
d76b87d6e3
Useful debug file output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4672 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 13:36:52 +00:00
28142408ff
Refactoring so that all counting in UGv2 is done on the filtered context. In particular, tests for empty pileups and too many spanning deletions now use the correct counts. Also, -all_bases mode now trumps all; this one is for you, chartl.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4671 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 05:01:12 +00:00
c7229abbf7
Get rid of 'meaningless and random values' that prevent Sendu from merging PG lines. I have to admit that he did have a good point there.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4670 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 03:35:12 +00:00
2fd816ac5f
Updated ordering of integration tests. GVC > VR > AVC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4669 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-14 06:33:28 +00:00
cb1e8ad43a
Temp bug fix for indel genotyper: if there are two or more variant contexts at a site, just choose the first one containing an indel and genotype that. There might be cases where IGv2 emits 2 indel variant contexts in at the same ref location which made us fail there. A better solution will be to form underlying haplotypes supported by reads and compute likelihoods of that.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4667 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-14 00:21:54 +00:00
82f9327b5e
Throw the right exception
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4666 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 22:18:42 +00:00
44d0cb6cde
New version of cutting routines for VQSR. Old code removed. Working unit tests. Best practice with testng integration test (everyone look at it). Walker test now allows you to not specify no. input files, if it can infer input counts from MD5s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4664 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 16:19:56 +00:00
62a106ca5a
Disabled VariantGaussianMixtureModelUnitTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4663 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 03:53:33 +00:00
673fa841a4
Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.
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Removed obsolete usages of PackageUtils with updated PluginManager.
Ported Queue interval utilities written in scala over to Sting's java IntervalUtils.
Added a very basic intergration test to ensure that the fullCallingPipeline.q compiles.
Added options to specify the temporary directories without having to use -Djava.io.tmpdir (useful during the above integration test).
While adding tempDir added options to specify the run directory from the command line, for example "-runDir v1".
Upgraded to scala 2.8.1 and updated calls to deprecated functions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4661 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 20:14:28 +00:00
42acc968b1
Unit tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4660 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 20:09:39 +00:00
b51762c279
When you commit code late at night you tend to make careless mistakes... like forgetting to update integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4658 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 14:41:10 +00:00
988da428ae
Bug fix for old style tranches file. ApplyVariantCuts moved over, and passes integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4657 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 14:38:26 +00:00
c5f8c4dd0d
VariantEval test for tranches file, plus cutting over VE to use the generic Tranches framework
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4656 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 13:52:40 +00:00
69de3e51bf
Better precision for the calculated AF value. Now looks at the total number of samples to determine how much precision is necessary. Also, changing default min BQ used for calling in UGv2 to Q17.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4655 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 08:31:40 +00:00
ec83a4b765
Initial commit, without any tool changes, of a new infrastructure for determining tranches. This new version walker up from the lowest quality snps and determines Ti/Tv. This is marginally more stable than moving in the other direction when there are few novel variants (exomes). Can make a substantial difference in the size of the call set (10-20%). I'll hook it into the main system now. Includes an new class Tranche, isolated read/writing utilities that are now testing in TestVariantRecalibrator, which should be moved to UnitTest as soon as I can figure out how to do this on my mac.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4654 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 23:52:49 +00:00
ed6396ed43
No longer getting the inet, it seems to potentially hang the JVM
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4653 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 23:49:42 +00:00
2f6666a988
Correcting traversal statistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4652 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 22:46:58 +00:00
dbde721dd0
Bug fix for filtered records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4651 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 18:54:51 +00:00
698e5cf345
for GATK style codecs, make sure we fill in their GenomeLocParser from the RMDIndexer
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4650 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 18:44:15 +00:00
2f3be24a00
Improvement in exact allele frequency calculation model (still under test, but this is definitely better than what I had before). Instead of approximating log(10^x+10^y) as max(x,y), approximate full Jacobian formula max(x,y)+log(1+10^-abs(x-y)) with static lookup table for the second term.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4647 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 01:22:35 +00:00
2e0296fef9
NWayOut logic slightly changed: 1) results.list file is gone; 2) now with -nWayOut one can specify either a) suffix to attach to every output file (i.e. cleaned reads from inputK.bam will be sent to inputK.suffix.bam) or b) *.map tab-separated file that must list <input_name> <output_name> mappings, one per line, for every input file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4645 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 20:32:16 +00:00
a1adfb91ce
And now @Hidden tags are really in place :-/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4644 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 20:28:40 +00:00
68ce55148e
(pseudo-)genotyping functionality added: force-emits calls (including REF) at specified locations. Currently @Hidden for testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4643 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 20:25:40 +00:00
8e36a07bea
Convert GenomeLocParser into an instance variable. This change is required
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for anything that needs to be simultaneously aware of multiple references, eg
Queue's interval sharding code, liftover support, distributed GATK etc.
GenomeLocParser instances must now be used to create/parse GenomeLocs.
GenomeLocParser instances are available in walkers by calling either
-getToolkit().getGenomeLocParser()
or
-refContext.getGenomeLocParser()
This is an intermediate change; GenomeLocParser will eventually be merged
with the reference, but we're not clear exactly how to do that yet. This
will become clearer when contig aliasing is implemented.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 17:59:50 +00:00
5ef4b234d8
Updates for broken integration tests. Counting annotations (AC, AF) now work correctly for AC = 0 sites
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4640 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-09 19:43:43 +00:00
4759fdd2ac
V1 of read and variant simulator and assessor. SimulateReadsForVariants generates BAM and VCF with given combinations of variant and read properties. AssessSimulatedPerformance produces a table suitable for analysis in R
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4637 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-08 21:01:33 +00:00
97db593efb
making my last commit message actually true
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4636 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-07 18:26:23 +00:00
be499fc986
making the reference optional (the GATK will set it on the first run if it's not included), and setting the seq index if they do supply it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4635 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-07 18:15:31 +00:00
e05af54f3e
Found the cause of 80% of our non-called FNs: an excess of filtered bases were causing us to choose the wrong alternate allele. More details to dev team.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4634 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-07 03:39:57 +00:00
2a8c97a4a7
better error catching, as well as allowing for default index naming, <filename>.idx
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4633 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-06 19:12:19 +00:00
cb2e26a004
by request, an indexer tool to create Tribble style indexes outside of the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4632 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-06 18:59:06 +00:00
bbb890dd6c
Bug fix for variants in VCF header fetching to avoid null pointer when a VariantContext tribble codec doesn't have a header
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4630 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-05 12:43:25 +00:00
c9dbd8f80a
Bug fix for Tim: all point events must be treated equally
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4629 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-05 03:42:51 +00:00
913db5d1ab
Unfortunately when annotating sites with the UG the -G None option was wiping out the single annotations added by -A options
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4625 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-04 19:27:23 +00:00
816c86776e
Walker description was wrong and it was bothering me
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4624 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-04 02:17:09 +00:00
87f6738d4c
Deprecated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4623 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-04 02:07:40 +00:00
42e9987e69
Bug fix to GenotypeConcordance. AC metrics get instantiated based on number of eval samples; if Comp has more samples, we can see AC indeces outside the bounds of the array.
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Bug fix to LiftoverVariants - no barfing at reference sites.
AlleleFrequencyComparison - local changes added to make sure parsing works properly
Added HammingDistance annotation. Mostly useless. But only mostly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4622 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-03 19:23:03 +00:00
3d27defe93
Fixed output stats (percentage denominator)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4621 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-03 18:47:06 +00:00
4e109f58bf
In preparation for Ryan's jumping into SLOD: getting rid of bad hack to ensure P(AF=i) is calculated in the strand-specific cases. With Mark's recent changes this is no longer necessary and just makes the code slower.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4620 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-03 03:44:59 +00:00
22d64f77ff
Added hidden --outputMultipleBaseCountsFile option to detect cases where a single read has more than one base at the same position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4619 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-03 03:22:48 +00:00
8f9bf82aa7
Bamboo is correctly interpreting test fails. Reverting forced-fail test
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code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4617 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-02 19:32:34 +00:00
1df166b76e
Forcing a unit test fail to ensure that Bamboo is picking up on failed tests
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as well as successes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4616 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-02 19:03:12 +00:00
a885ecf046
When merging MNPs, the phased flag and the phase quality (PQ) are determined simultaneously
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4613 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-02 14:44:26 +00:00
861ee3e37a
Changing testing framework from junit -> testng, for its enhanced configurability.
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Initial test to see how Bamboo will respond. More detailed email to follow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4609 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 21:31:44 +00:00
fe3f78e1d3
make it full (absolute) path for the file names recorded in results.list
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4608 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 20:53:51 +00:00
2ac5e55130
typo
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4607 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 20:38:02 +00:00
0e6dd38936
In n-way-out mode, added printing names of all the output files into 'results.list' file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4606 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 20:37:38 +00:00
64599d1074
Added debugging message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4605 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 19:51:42 +00:00
639ecdc931
Noted in comment that using a single sample in MergePhasedSegregatingAlternateAllelesVCFWriter does NOT update any of the INFO fields, though this could be changed in the future...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4604 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 19:02:52 +00:00
8439f0aa61
Check for VCFConstants.MISSING_VALUE_v4 when retrieving INFO fields and consider such values as non-existent
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4603 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 17:51:35 +00:00
aadd230636
N-Way-Out is back. Now uses SAMReadID to identify each read's source bam, so should be reliable. Interface is sort of ugly fo now: to generate output file names, .bam is stripped from input file names, then the value of -nWayOut argument is pasted on (and all the output files are written into the current dir).
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Unrelated change: in the sorted-target mode (when we read sorted target intervals one by on from a file), one can now specify multiple semicolon-separated interval files (all must be sorted). Not hugely useful probably, but makes --targetIntervals always process its values in exactly the same way, so we are consistent (it has been already taking ;-separated args in unsorted mode)
NwayIntervalMergingIterator: reads in multiple sorted GenomeLoc input streams (iterators) and presents them as a single sorted and merged stream
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4602 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 16:06:51 +00:00
23cb399a88
Reasonable first pass at a correct SB calculation. Simple utilities to support it. VariantsToTable no longer prints filtered sites by default. New non-standard variant eval module to print comp sites not present in eval (FN finder)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4601 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-31 12:41:52 +00:00
30fae5cf18
Major redo of exact AF computation for UnifiedGenotyperV2. Fact of life is, there's no way we can compute an exact QUAL field and keep performing the AF computation in linear probability space. In good sites with lots of samples, the ratio of Pr(AC=K*|D) to Pr(AC=0|D) can be 10^1500 or some ridiculous large number like that, which no double can represent. So, we abandon probablity space and work now in log likelihood space, which has several major repercussions:
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a) Sites were numerically well behaved now, but another hard fact of life is that the AF iteration is defined in linear Pr space, not in log likelihood space, and the math doesn't work out in log space. So, we need to convert back and forth from lin to log space.
b) As a consequence of a), the code got a major slowdown, and calling the 629 samples was about 15 times slower than before (sic).
c) To solve b), log10 of integers are now cached at init, and numerical approximations are now made. Most importantly, I'm using the approximation that log(exp(a) + exp(b)) ~= max(a,b) which seems almost inconsequential in practical performance but reduces computation time to what it was before. More detailes analyses are forthcoming. This approximation can be refined further on to avoid expensive log-exp conversions if further profiling and analysis deems it necessary.
Also, two other issues were solved:
a) Strand bias computation was actually wrong in the case where the optimal AC was bigger than max(forward reads,reverse reads). Now the code is exactly as buggy as the grid search model (all bugs are equal, but some are more equal than others)
b) Genotype likelihoods are now computed in a better way and if a likelihood < 0 we don't just cap to 0 but do something a bit smarter.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4600 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-31 01:26:04 +00:00
d492621122
The TraversalEngine's habit of hanging onto old ROD states seems to have a bad
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interaction with Tribble. In Tribble, keeping these references in memory until
the shard is flushed means keeping one 512K character buffer per object in
memory. Fixed by purging the reference to the object at the end of the
shard traversal.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4599 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-29 17:09:58 +00:00
1c056ea791
Users can now use VariantAnnotator to add annotations from one VCF to another. For example, if you want to annotate your target VCF with the AC field value from the rod bound to CEU1kg, you can specify -E CEU1kg.AC and records will be annotated with CEU1kg.AC=N when a record exists in that rod at the given position.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4598 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-29 16:38:31 +00:00
1b3fc8ddd2
Doing things too quickly is also naughty. Thanks, Andrey. Now, we're even.
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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
58f7b4c595
Naughty use of assertions means that malformed records are not caught.
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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
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.
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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
depristo
delangel
hanna
chartl
handsake
ebanks
kshakir
fromer
asivache
rpoplin
aaron
bthomas