b316c9a590
Renamed StratifyAlignmentContext to AlignmentContextUtils, and StatiefyContextType to ReadOrientation. Also, went through the system and deleted all references to second bases. That ship passed long ago. This was the actual commit, the last was an intellij error
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5564 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-03 15:36:17 +00:00
5cca100aea
Eliminated the redundant StratifiedAlignmentContext, which previously just held a ReadBackedPileup, and made all of the class methods here just static functions. Far more logical organization, and avoided O(N) endless copying of data for the COMPLETE context. Many tools have been trivially reorganized to take an alignment context now. Everything passes integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5562 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-03 14:20:43 +00:00
98798eb276
Adding ReadPos rank sum test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5560 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-02 22:28:41 +00:00
09e89c8c97
Adding ReadPos rank sum test. Transitioned rank sum tests over to using Chris's implementation in order to harmonize the codebase. There isn't any reason to have competing implementations of rank sum. Thanks to Chris for adding the necessary hypothesis testing options. WilcoxonRankSum.java will be deleted soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5559 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-02 22:26:35 +00:00
11822da578
Stand alone, GATK dependent tool that Reads a list of BAM files and slices all of them into a single merged BAM file containing reads in overlapping chr:start-stop interval. Highly efficient when working with thousands of BAM files. Can merge 1MB of sequence of 1600 4x BAMs in 4g in only 2 hours.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5558 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-02 13:41:29 +00:00
27bfec785e
Some walkers for printing FASTA of reference for bed ROD, and "inverting" a bed file (finding regions not covered in bed)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5554 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-01 21:13:51 +00:00
0927b7c297
Fix for bug GSA-441: BAM file list with blank lines gives a confusing error
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message. Lines containing only whitespace in .list files are now ignored.
Also added support for comments in .list files: lines whose first
non-whitespace character is '#' are now also ignored.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5550 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-01 15:04:35 +00:00
4f8411f4b5
Revved Picard to access new flag to disable mmap for bam indices. Only added a 3% speed boost but the mmap was added to the heap count, making it harder to specify/restrict the total resident memory size in LSF. Specifying -Xmx4g will now stay much closer to 4g resident memory usage versus bumping up to 9g when accessing 900 x ~8Mb bai's.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5549 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-01 01:40:41 +00:00
df53351b0f
Get rid of score cutoff at 0 in the alignment matrix (i.e. score[cell] = max(0, score[from_parent_cells]). Use the computed score as is. Technically, it's pretty much NW now, not SW.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5548 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-01 00:11:04 +00:00
0a772688fe
implementation of the Gatherer class for CountCovariates, which makes it now scatter/gatherable. Kudos to the @Gather annotation Khalid just introduced!
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QuickCCTest is my test script for the gatherer.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5547 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-31 21:15:21 +00:00
dac1309dbd
Added two modes for selecting variants at random (random sampling).
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-number N -- generates a VCF with exactly N randomly chosen variants with equal probability.
-fraction F -- generates a VCF with approximately F (between 0-1) randomly chosen variants with equal probability. (Similar behavior to RandomlySplitVariants walker).
The reason for two modes is that the first one may need a lot of memory if your sample size is too large. The wiki is being updated with this information now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5545 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-31 21:12:40 +00:00
8a3b7d88aa
It was returning 1 when it should return 0
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5544 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-31 20:50:38 +00:00
c7445a6fbd
Now that logging is so standard, only prints messages about logging to DEBUG. Also, found a way to silence the mime.types warning, that doesn't matter at all to us.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5543 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-31 16:49:39 +00:00
7b452ea2b9
Fix for bug GSA-430: Can't specify same BAM file twice on the command line. An ArgumentException with an appropriate error message and a list of the duplicate BAMs is now thrown in this case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5542 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-30 22:23:24 +00:00
deab9f0aa5
Initial work on proto-shard merger:
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- create size() method that returns an approximation of the uncompressed size in bytes of BAM span.
I'll use this method as a protoshard weighting function until we determine how to normalize the
weights across the different data access mechanisms (reads, reference, RODs).
- Implementations of basic union/intersection/subtraction mechanisms for BAM spans; should be enough
to get an accurate weight for two proto-shards put together.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5541 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-30 22:03:43 +00:00
328f89f66a
Minor changes to MannWhitneyU:
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- Comment fixes to better explain why two-sided test wants to use the LOWER (not higher) value for U
- Much more direct testing of MWU functions
- Uniform approximation was always using the < cumulant (sometimes the > cumulant should be used instead)
- Uniform approximation currently not used (regime in which it was being used was not the right one -- not necessarily bad, but not an improvement over normal)
+ this particular approximation is for major imbalances of the form m >> n. Code may be altered in the future to use this method for this particular regime, if the method's not too slow.
- Hook into one-sided test.
RegionalAssociationRecalibrator: NaNs were being caused by presence of Infinity and -Infinity values out of the walker. Currently I'm just re-setting them to arbitrary post-whitened values, but the walker will be changed to prevent output of these values, and the "fix" will undone.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5539 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-30 17:03:02 +00:00
fff11a3279
No more pesky NaNs for norms ( HINT::: ((double) x) == Double.NaN is NOT (somehow) the same as Double.compare(x,Double.NaN) == 0). Effectively reverse sorting by changing (rank/size) to ((size-rank)/size).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5538 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-29 22:43:24 +00:00
5d26c66769
Count Covariates is almost scatter-gatherable now!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5537 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-29 22:25:33 +00:00
5ddc0e464a
Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5536 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-29 21:04:09 +00:00
0f4ace0902
fixed a bug when the concordance track doesn't have the sample in the variant track.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5535 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-29 18:24:19 +00:00
f6dfdc7f3b
Single-tailed hypothesis testing in MWU
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5533 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-29 15:53:40 +00:00
8ae14793f2
Small standalone utility to aggregate BGZF block statistics in a BAM file.
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Works in the same coordinate space as BAM chunks, so this will be used to
calibrate chunk weighting.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5531 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-28 22:25:45 +00:00
f3e4c24f63
Framework works properly now, but whitening still has a kink which is that the covariance matrix gets re-sorted automatically by the eigendecomposition, so somehow the association between eigenvalue and dimension (e.g. association track) needs to be maintained throughout.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5530 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-28 22:22:37 +00:00
4c04c5a47a
Addition of a BedTableCodec to allow for parsing of Bed-formatted tables (e.g. bedGraphs). Fixes for the recalibrator. Implementation of the data whitening input. Some TODOs in the RAW.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5529 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-28 21:35:09 +00:00
f2d84bf746
Changes the validity declaration from a true to false to a five point scale
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5527 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-28 18:31:53 +00:00
cd8321cdc9
Removed the completely unused generic but extremely expensive infrastructure for dynamic LocusIteratorFilters. Now the one, and probably only useful one, is called directly in the LocusIteratorByState itself to filter adaptor bases from reads. This shaves 10% off the runtime of all walkers, apparently. Has the additional benefit of eliminating a lot of complex infrastructure that resulted ultimately in only a single function call.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5525 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-27 20:48:24 +00:00
231d095316
A clean, fast way to compute fragment pileups. Now consumes no CPU time at all. Ready for general use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5524 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-27 14:26:29 +00:00
6a1d12cf7b
Intermediate commit refactoring FragmentPileup to (1) make it more accessible (now in utils.pileup) as well as (2) improve performance. Passes all integration tests now. Upcoming refactoring will change further how the system can be accessed, and further improve performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5522 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-27 12:42:22 +00:00
3bcd4c5d75
--simplifyBAM is now in the SAMFileWriterArgumentTypeDescriptor, as suggested by map. PrintReads has an integrationtest now that writes out a 1 MB bit of HiSeq normally, with compress 0, and with simplifyBAM on.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5521 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-26 14:57:18 +00:00
28ae53d796
Merging the best parts of Mark's fix for the O(n^2) algorithm and my
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concurrently-written fix for the same.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5520 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-26 13:32:23 +00:00
d8fbda17ab
O(N^2) bug found and removed -- very subtle and hard to find. ArrayLists underlying read backed pileups were being initialized with size() from the entire pileup up all samples, not the sample-specific sizes. So in 1000 samples at 4x, we were creating 1000 x 4000 element array lists, instead of 1000 x 4x element array lists. This fix results in a 2-3x speedup for 900 sample calling, and moves UG.map() back into the main CPU cost of UG with many samples.
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900 samples in a single BAM:
Release: 64.29
With sample-specific size: 24s - 35s
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5519 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-26 12:38:19 +00:00
7272fcf539
Now uses the NO_HEADER option to avoid breaking MD5s due to changes in GATKArgumentCollection
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5518 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-26 12:00:37 +00:00
27c8fb1e4d
Added support for a general GATK option --simplifyBAM to automatically remove and simplify kept reads in an output BAM file. Specifically, duplicate, non-PF, and unmapped reads are removed, and all extended tags in the retained SAM records are removed except the RG:Z tag. This option is very useful when creating temporary BAM files (merged per-population or multi-sample cleaned) for future calling (as in the 1000G processing pipeline). Results in a significant reduction in space of the resulting BAM, faster reading of the BAM, and surprisingly even faster UG performance:
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1-10mb of chromosome one, from NA12878 HiSeq 64x data set on hg18:
Full BAM
Write time: 8.6 m
Size: 866M
CountReads time: 2.9 m
UG time: 11.3 m
Simplified BAM:
Write time: 6.2
Size: 458M
CountReads time: 85.7 s
UG time: 10.1 m
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5517 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-26 01:21:35 +00:00
fc8acd503e
Enabled the parameterize option for debugging PipelineTest MD5s.
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Fixed escaping expressions that have more than one space between arguments.
Updated example to match the wiki.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5516 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-26 00:41:47 +00:00
fe7f45ee2e
First pass at recalibrating associations, with optional data whitening. Modification to the TableCodec so it can natively read bedgraph files (just needed to add an extra header marker: "track").
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5515 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-25 19:35:39 +00:00
ac39f5532e
Turn off index caching.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5514 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-25 18:48:23 +00:00
8d8aed6a67
Fix correctness issue when dynamically merging many files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5512 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-25 16:35:43 +00:00
c9283e6bc5
Refinement to previous commit: no need to duplicate code to annotate rsID since variantAnnotatorEngine is called from UG anyways.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5511 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-25 15:00:32 +00:00
3383733379
Same commit as previous one for VariantAnnotator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5510 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-25 12:07:18 +00:00
8701dfe8d3
Hideous, horrible, hairy mutant bug: when we annotate ID field in indels, we were looking for SNP records matching the position, instead of indel records.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5509 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-25 12:04:08 +00:00
3e3ff4a9e7
Bam gathering passes on the compression_level and the create_index flag to MergeSamFiles.
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VCF gathering passes on the no_header and sites_only flags to CombineVariants.
Fixed deletion of gathered log files. Although they are intermediate and do not need to be re-run if not present, they should not be deleted.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5508 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-25 03:58:38 +00:00
47279ee56e
Added --concordance option that outputs the intersection between two VCF files. Useful to see what calls were made in both technologies/algorithms.
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Wiki has been updated accordingly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5507 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 21:27:16 +00:00
e47513f043
Minor updates to match the wiki documentation.
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Upper cased the PartitionType enum values.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5506 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 20:22:23 +00:00
f3e94ef2be
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.
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JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar.
JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar.
Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath.
Walkers from the GATK package are now also embedded into the Queue package.
Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP.
Removed the GATK jar argument from the example QScripts.
Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts:
1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers.
2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3
Removed other unused code.
Re-fixed dry run function ordering.
Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 14:03:51 +00:00
18271aa1f4
It never fails to amaze me that aligners can find so many different ways to place indels off the ends of contigs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5503 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 04:17:23 +00:00
48b15d42e0
More fixes and improvements. We no longer use any bases under Q20 because random ~Q5s were cluttering the graphs; instead we grab any contiguous segments of size at least MIN_SEQUENCE_LENGTH where all bases are above Q20. Also, I implemented a quick algorithm to traverse the graph (using DFS) to choose the two best scoring paths (haplotypes). Used it successfully at NA12878 HM3 SNP sites to determine whether they are homozygous (no distiction yet between ref and alt) or heterozygous! Indels are the next target. Still have some issues to work out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5502 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 03:51:19 +00:00
26e3bea76e
Fix for == used to test object equality.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5499 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-23 18:15:19 +00:00
401d1cb97f
Bug fixes plus some debugging code added. Broke out DeBruijnVertex into its own class so that the interface is now cleaner. Still very much a work in progress.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5498 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-23 17:35:34 +00:00
37fbf17da8
Finally restored code after accidentally removing three days worth of work:
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schedule file infrastructure has been restored, and is now a single file.
Only the exact bins required for the traversal are stored in the schedule.
Very close to being able to merge schedule entries.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5497 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-23 05:52:40 +00:00
69646ff840
... and the corresponding integration test update
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5496 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-23 01:58:07 +00:00
ded80e0c57
Trivial change to remove space at the end of the description
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5495 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-23 01:47:46 +00:00
3414bccb46
documentation changes to agree with the wiki
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5494 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-22 21:48:49 +00:00
28149e5c5e
GenotypeAndValidate version 2, ready to be used.
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- now it differentiates between confident REF calls and not confident calls.
- you can now use a BAM file as the truth set.
- output is much clearer now
dataProcessingPipeline version 2, ready to be used.
- All the processing is now done at the sample level
- Reads the input bam file headers to combine all lanes of the same sample.
- Cleaning is now scattered/gathered. Inteligently breaks down in as many intervals as possible, given the dataset.
- Outputs one processed bam file per sample (and a .list file with all processed files listed)
- Much faster, low pass (read Papuans) can run in the hour queue.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5493 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-22 20:18:02 +00:00
687b2e51b4
Switch from togglable wiggle output to togglable bedgraph format. Can be pulled directly into IGV to show the statistics values. I'll need to bug jim to allow value-toggling in a bedgraph, currently 2nd and 3rd columns are just ignored.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5492 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-22 17:58:53 +00:00
5a79f16ea4
Fixed an edge case where an exception was thrown if either of the sets was empty for the MWU test. Also altered the output format so U itself is not printed (which though interesting, isn't so useful for recalibration), but rather a value I call V (really the deviation of U from its expectation).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5490 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-22 16:28:44 +00:00
af7f78e8ba
Minor debugging output change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5488 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-22 12:59:26 +00:00
b463faad92
Fixing typo
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5487 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-22 03:57:11 +00:00
1a9e65bcd4
Updating other walkers now that VCC extends from VC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5486 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-22 03:10:40 +00:00
0ee687e49d
For Mauricio: now, even in GENOTYPE_GIVEN_ALLELES mode, the VariantCallContext (which now inherits directly from VC) will report reference calls as confidently called if they pass the threshold even if the QUAL of the record itself is low because we were forced to have an ALT allele.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5485 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-22 02:42:28 +00:00
ab6a815184
As per the comments in the commit itself: when reads get mapped to the junction of two chromosomes (e.g. MT since it is actually circular DNA), their unmapped bit is set, but they are given legitimate coordinates. The Picard code will come in and move the read all the way back to its mate - which can be arbitrarily far away and cause records to be written out of order. Very evil.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5484 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-21 20:30:24 +00:00
d9202f2764
Don't try to create a GenomeLoc from an unmapped read
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5480 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-21 13:46:55 +00:00
1c95208e26
Finally found the bug that everyone is reporting on GS. Iterators on PriorityQueues aren't guaranteed to return elements in sorted order (a pretty stupid contract) - so we were passing items to the constrained writer out of order. Just do a Collections.sort instead (1 line of code). Happy father's day!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5476 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 21:28:19 +00:00
9568c84af9
Don't output these messages in INFO mode because they are scaring people unnecessarily
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5475 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 19:55:22 +00:00
22ff2573d5
Removed MAG entirely
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5474 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 19:43:23 +00:00
55897631ad
Initial attempt at identifying potentially interesting variants in a Mendelian disease context when the called genotypes are uncertain.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5473 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 19:41:35 +00:00
b2b8a4f19f
Re-un-final'ed BAQ.MAG as it was pre r5469.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5472 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 19:40:31 +00:00
1d5326ff0c
Minor fixes to the cmd-line help messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5470 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 18:18:04 +00:00
7857cb5a22
Waiting to go to the hospital -- fixed a bug in the BAQ calculation where the BAQ would NPE if a read had no usable bases (all clipped, for example) but didn't fail the PF filter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5469 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 17:45:21 +00:00
e84a27ceea
OverlapWithBedInIntervalWalker calculates the average per-input-interval coverage by the BED intervals track
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5468 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 17:44:46 +00:00
abc7d1aef9
BeagleOutputToVCF now accepts an option to keep monomorphic sites. This is useful to genotype a single sample, where having AC=0 just means that the sample is hom-ref at the site.
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ProduceBeagleInputWalker can optionally emit a beagle markers file, necessary to use the beagled reference panel for imputation. Also supports the VQSR calibration curve idea that a site can be flagged as a certain FP, based on the VQSLOD field. This allows us to have both continuous quality in the refinement of sites as well as hard filtering at some threshold so we don't end up with lots of sites with all 1/3 1/3 1/3 likelihoods for all samples (i.e., a definite FP site where we don't know anything about the samples).
Added a new VariantsToBeagleUnphased walker that writes out a marker drive hard-call unphased genotypes file suitable for imputating missing genotypes with a reference panel with beagle. Can optionally keep back a fraction of sites, marked as missing in the genotypes file, for assessment of imputation accuracy and power. The bootstrap sites can be written to a separate VCF for assessment as well.
Finally, my general Queue script for creating and evaluating reference panels from VCF files. Supports explicitly genotyping a BAM file at each panel SNP site, for assessment of imputation accuracy of a reference panel. Lots of options for exploring the impact of the VQS likelihooods, multiple VCFs for constructing the reference panel, as well as fraction of sites left out in assessing the panel's power.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5467 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 03:08:38 +00:00
9b8d41160b
GENOTYPE_GIVEN_ALLELES now respects the filter status of the incoming alleles file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5466 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 02:59:28 +00:00
6281c1db6f
A nicer error (UserException now) for malformed genome locs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5465 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 02:58:29 +00:00
b45afe5ba8
Several major fixes and changes to new indel likelihood model:
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a) Scrapped the way in which we constructed candidate haplotypes because it wasnt fully correct and yielded corner conditions with incorrect genotyping and likelihood computation. Ideally, a haplotype should "cover" the read and the most likely alignments should be such that the ends of the read are inside the ends of the haplotype. This wasn't happening, and if you have a "dangling read off a haplotype" the probabilistic alignment model may prefer to shift a read instead of scoring it correctly - this is especially bad with tandem repeat insertions.
So now, we build haplotypes based on the reference context and adaptively change them based on read alignment positions, plus some padding and uncertainty in the alignment.
b) Changed the way soft clipped based are dealt with. Instead of either ignoring them or using them, we only use them if the read start or end position (after soft clipping) are within eventDistance of the current location. This is done because it's very common that BWA's strictly local SW implementation will soft clip every single read at an insertion position because it couldn't place that end of the read without too many mismatches, but the read is legit and the bases are good quality. If we don't take these bases into consideration, reads which are informative of an insertion event are essentially discarded because the informative part is clipped away.
c) Several cleanups and fixes to the context-dependent gap penalty model based on length of HRun.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5464 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-17 18:39:31 +00:00
cd38dfb4ef
Now with a clearer, grammatically correct message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5462 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-17 18:06:05 +00:00
10466dc7d1
I finally broke down and added a default documentation string to @Input for use in Queue scripts. It's not ideal, but I couldn't take any more queue scripts with doc="x" all over the place.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5461 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-17 18:05:25 +00:00
c1798a7dbc
Whitespace cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5460 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-17 18:04:08 +00:00
30237e6824
Updated the walker to specify the build based on the user's input file name if the user does not specify the build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5459 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-17 17:49:17 +00:00
3de300e504
A walker that moves annotations from the filter field to the info field of truth annotated vcfs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5458 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-17 17:11:28 +00:00
481750cbf9
Probable patch to Jerry Glenn's GetSatisfaction report. I'm having him test it out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5456 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-17 16:00:50 +00:00
3eea6e92b7
An extremely basic implementation of a deBruijn-based local assembler, using the jgrapht graph library. This is not at all optimized and has only been tested on my very simple 3-read test bams. I'm sure there are bugs in there - more testing coming soon. Insertions and deletions confirmed to generate identical graphs (except for the multiplicity of edges of course). Not worth using yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5455 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-17 14:03:07 +00:00
28a5a177ce
Very crude implementation of writing BAM 'schedules' to disk rather that 'meta-
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indexes'. Not yet elegant, but proves that it circumvents the performance
issues associated with the meta-index.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5454 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-16 21:48:47 +00:00
8d0880d33e
Misc cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5453 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-16 17:33:19 +00:00
c6ef6ee8b7
Recal file is in input to ApplyRecalibration not an output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5452 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-16 12:08:58 +00:00
8e89ff170e
Can't check substitution type of tri-allelic SNPs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5451 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-16 03:06:03 +00:00
e2e435d52c
GenotypeAndValidate: now looks at annotations in the INFO field instead of filter field. Better output and filters repetitive calls to indel extended events.
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IndelUtils: added a isInsideExtendedIndel() method to filter the above mentioned.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5449 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-15 21:54:40 +00:00
d98503ca50
Removing some debug code from VQSRv2. VariantEval can now be stratified by contig with -ST Contig. New hidden option in CombineVariants for overlapping records to take the info fields from the record with the highest AC (while still updating AC/AN/AF correctly) instead of dropping info fields which aren't exactly the same.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5448 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-15 21:28:10 +00:00
4b9b767eb1
SelectVariants: now keeps the YAML stuff internal... it's there if you wanna use it, but won't be published anymore. Official parameter is the string for now.
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VariantEval: now sports the new MendelianViolation utility class.
MendelianViolationClassifier: I noticed I had broken chartl's walker by changing VariantEval, so I took the liberty to modify it to use the new library too, though I kept modifications to a minimum, could have gone into full integration if this is a useful tool, but since it's in oneoffs, I decided not to go all out.
MendelianViolation: Some getter methods were added for chartl and VariantEval.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5447 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-15 18:36:55 +00:00
653fb09bb7
a) Next iteration of context-dependent gap penalty model for new probabilistic alignment indel model. Actual model is now implemented, computes homopolymer run profile for candidate haplotypes and looks up in table gap penalties based on hrun length at each position. Initial penalty model is a very naive affine penalty model with each extra hrun increment decreasing Q2 the gap open penalty, until a minimum is reached. Still needs to be tuned and ideally get data from recalibration.
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b) small bug fix when setting debug arguments
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5446 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-15 16:46:28 +00:00
bbcc4ed700
The second pass of the contrastive VQSRv2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5444 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-14 21:05:02 +00:00
2a2538136d
A version of VQSRv2 that does contrastive clustering in two passes. The walkers will be renamed when they are moved to core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5443 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-14 21:03:56 +00:00
fcc347bb05
making sure the output is as pretty as I said it would be on the wiki.
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wikipage for this walker is up, at : http://www.broadinstitute.org/gsa/wiki/index.php/Genotype_and_Validate#Examples
use it ;)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5442 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-14 20:32:09 +00:00
239dae0985
Absolutely nothing to get excited about. This is just the skeleton for the local assembler. It doesn't do anything at all now except for collect reads over each -L interval and pass them to an assembly engine (which isn't implemented yet). The interface for the AssemblyEngine will change later, but for now this one is the most conducive to debugging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5441 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-14 20:31:54 +00:00
6d09cdd4bc
This is a walker that lets the user generate the bed file for declaring variants true positives or false positives. For use with the IGV crowd sourcing project.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5440 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-14 19:56:16 +00:00
f75ad0dee3
Now in Picard, and released to the public
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5439 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-14 19:36:56 +00:00
9dfe4c9cb7
moving GenotypeAndValidate to the playground. It's ready to be used.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5438 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-14 19:19:18 +00:00
33c7593218
YAML integrated mendelian violation utility class, integrated and tested through select variants. Wiki is updated.
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ps: I moved it out of tribble. If you think it should reside in a different place, just yell at me.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5436 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-14 16:43:37 +00:00
5406e779d2
Ryan noticed that I accidentally killed a public interface method for getting tag information.
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Reinstated. Proper unit test to follow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5434 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-14 15:51:19 +00:00
3e3ec85807
Checked for consistency with the previous integration tests, and updated the walker and test to use the new I/O system (always prints 4 digits on floats.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5433 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-13 15:24:22 +00:00
b99e27bf9b
In the process of optimizing ProduceBeagleInputWalker, discovered that the GenotypeLikelihoods, the UG, and Genotype objects were using old-style GL tags internally, and then converting from Likelihoods -> GL String -> Likelihoods -> PL String throughout the GATK. It was both painful and led to convoluted code throughout the system. Removed everything but GL conversion -> PL in the GenotypeLikelihoods objects, and now all of the codes in UG now immediately provides GenotypeLikelihoods to the Genotype objects, which is converted straight to PL now. Resulted in a 30% speed up in ProduceBeagleLikelihoods, passes integration tests without any modifications, and likely speeds up writing any VCFs with likelihoods.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5432 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-13 00:07:51 +00:00
ceb08f9ee6
Moving some math around in VQSRv2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5431 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-12 15:15:05 +00:00
d01d4fdeb5
Optimized version of produce beagle tool, along with experimental (hidden) support for combining likelihoods depending on estimate false positive rate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5430 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-12 02:06:28 +00:00
ee8f2871f7
A better output for Genotype Concordance summary. Now does only % comp hom-ref called hom-ref, het called het, and hom-var called hom-var, which are the quantities we typically show in slides. Updated intergration tests to reflect this change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5429 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-12 02:03:48 +00:00
93de326066
Added a new @PartitionBy for walkers to specify how to cut up their inputs.
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Now building all javadoc.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5428 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-12 01:33:08 +00:00
8ca3390ee0
Low level plumbing work required to have a context dependent error model with the new indel probabilistic alignment model. This just adds an extra input argument and does some refactoring so that when an actual model is ready it will be easy to plug in.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5427 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-12 00:00:55 +00:00
e35a67b3cc
changed the name of the parameter to make the wiki more uniform.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5426 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-11 17:54:53 +00:00
4a84a81d17
SelectVariants: added parameters for mendelian violation. Given a trio vcf, it will generate a VCF with the sites that are mendelian violations.
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GenotypeAndValidate: now annotates the validations with callStatus.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5425 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-11 17:47:53 +00:00
b03055099a
a) Changed the way we classify and log indel events (e.g. in IndelClasses table inside IndelStatistics VE module). Made names clearer, and split logging of event length with number of repetitions of event.
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b) Add an experimental annotation to log indel type string inside the INFO field, just for debugging/temp analysis purposes (will consider making it standard if it proves useful).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5424 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-11 17:37:41 +00:00
b3464a6031
Initial commit of VQSRv2 that passes the old integration tests. Not ready to be used yet unless your name rhymes with ... oh wait, that's me.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5419 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-11 15:18:34 +00:00
ccc773d175
Refactoring, cleanup, and performance improvements to ProduceBeagleInput. It's really a shame that there's no integration tests...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5418 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-11 13:55:30 +00:00
097a9a59e8
Updated LSF libraries to use Pointer instead of Structure.ByReference for struct arrays since the the latter is autoRead() and LSF doesn't always return null for empty arrays.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5417 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-10 22:58:54 +00:00
4baeb5979f
It turns out that Math.log10() can return 0, which leads to QUALs being set to -0, which is off-spec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5415 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-10 03:08:56 +00:00
3596c56602
New attempt at the constrained movement version of the indel realigner (I've kept around the old writer for now). The new contract is that the realigner must ask permission before trying to clean an area; permission will be denied by the CM-Manager if it was required to flush its cache of reads because of too much depth within a distance of maxInsertSizeForMovingReadPairs. Added integration tests to cover different max cache sizes, including an expected exception when too small a value is chosen. The actual logic changes were fairly minor - much of this commit is really just some cleanup. I'd like to throw 1000G Phase I at it, but will respectfully wait for Ryan to hit his deadline before doing so.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5414 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-10 02:48:29 +00:00
ff7edc4493
Minor bug fix in empiricalMu prior calculation in VQSR.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5412 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-10 00:42:38 +00:00
0b45de14ed
Some minor updates to fully utilize the functionality of reduceByInterval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5411 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-09 20:38:08 +00:00
509daac9f7
Minor bug fix in k-means implementation. Updating VQSR integration tests in preparation for VQSRv2 by removing some unused features such as VariantDatum.weight and ti/tv cutting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5410 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-09 00:26:28 +00:00
fa7284b7a1
Genotype And Validate walker is now ready to be used by anyone.
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given an annotated VCF and a BAM file, it genotypes (using the reads in the BAM) each variant in the VCF (for snp or indel) and validates (or not) the 'known' annotation. Outputs a truth table with the PPV and NPV values, and optionally a vcf file with the variants that had enough coverage to be validated. You can optionally provide a minimum depth of coverage and only do the analysis conditional on that. (will write a wiki for this walker, as it might be useful for future validation essays).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5409 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-08 22:10:38 +00:00
da88c29b6e
Added a module to test for reference mismatch associations, and a self-normalized/self-normalizing version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5408 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-08 20:01:28 +00:00
31a2575c7b
Fixes:
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- Don't know how I got the wiggle header so utterly wrong. Fixed.
- Q-values now have a static maximum of 2000 so IGV averaging won't make everything look spikey and ugly.
- Changing windows to size 100 for (hopefully) better resolution.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5406 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-08 17:16:21 +00:00
1b310401fe
Due to the approximation not being well-founded in this case, (and the non-existence of a pre-computed table at this time), pushing up the cutoff
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5405 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-08 16:24:42 +00:00
00ac51acc8
Added several integration tests for UG indel caller:
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- Basic
- Multiple technology
- Test minIndelCnt parameter
Added also 2 disabled tests:
- Parallelization: issue w/code right now is that if -nt > 1, filter field shows "PASS" instead to ".", cause TBD
- Genotype given alleles mode: code not working yet.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5404 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-08 16:21:21 +00:00
77fe902dbd
Testing modules now use wider windows and heftier shift, hopefully this will remove some of the noisiness of the results. Some UStatistics were changed to TStatistics to try and limit noisiness as well. Walker will also additionally write out wiggle files directly (which can be converted into "proper" tdf files via igvtools tile [args] [in].wig [out].tdf [ref]) subject to some restrictions. MWU could get stuck in a long-running recursive regime, it'd be nice to have a table lookup or a good small-n large-m approximation, for now the uniform should work just fine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5403 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-08 15:26:13 +00:00
b733cba7c7
re-fixing for a different approach suggested by eric!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5402 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-08 04:54:49 +00:00
d0598c7a04
Somehow missed this test when I was updating the md5s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5400 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 23:53:42 +00:00
b6339967f8
Updated GenomicAnnotator integration tests to include the -NO_HEADER argument so that they tests op yelling about trtrivial differences
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5398 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 23:07:01 +00:00
85ff983a59
Failed to include some required GenomeLoc utilities in my last commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5397 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 23:00:17 +00:00
02006954bc
UG: small bug fix when creating empty variant contexts in UG for the -EMIT_ALL_SITES to allow indels.
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GAV: First version of the walker that validates reads from a BAM file based on an annotated VCF with TP/FP annotations.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5396 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 22:51:04 +00:00
9384b2ff65
A few quick fixes to temporarily make the LowMemorySharder return exactly the
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same shards as the previous sharder, so that I can directly compare filespans
to see where some performance bugs lie.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5395 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 22:43:14 +00:00
0b4e51317b
Now includes project consensus high sensitivity data set
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5394 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 20:52:11 +00:00
43056d0188
Fixed integration test to reflect changes regarding when comp tracks got subset to fewer samples and whether no-call sites would get pulled in for comp tracks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5393 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 20:25:57 +00:00
73e43d8d2c
Added functionality:
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-disc (--discordance) parameter together with a ROD track will output a VCF with the variants in the ROD track that are not present in the 'variants' VCF. Useful tool to list the variants from hapmap (for example) that weren't called in a dataset.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5392 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 19:18:15 +00:00
dc33fbed7c
Switched the CVUnitTest broken info from an Integer to a String since as of r5383 Integers are no longer broken when converted to Floats.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5390 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 16:33:14 +00:00
8c262eb605
Initial commit of new likelihood model to evaluate indel quality. Principle is simple, a plain Pair HMM with affine gap penalties (in log space) that does quasi-local alignment between reads and candidate haplotypes and which in theory should be more solid and more reliable than the older Dindel-based model. It also allows to be easily extensible in the future if we decide to introduce either context-dependent and/or read-dependent gap penalties.
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Model is disabled by default and we're still using the old Dindel model until I'm more confident that new model is a definitive improvement, so right now this is enabled by hidden command line arguments, and it's not to be used yet.
In detail:
a) Several refactorings to share softMax() available to other modules, so its now part of MathUtils.
b) Refactored a couple of read utilities and moved from BAQ to ReadUtils.
c) New PairHMMIndelErrorModel class implementing new likelihood model
d) Several new hidden debug arguments in UAC.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5389 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 15:31:58 +00:00
96fe540d66
Removing .tmp~ file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5388 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 14:52:38 +00:00
92045ecaa6
Finally figured out what data in the LSF C API call lsb_readjobinfo is causing JNA to SIGSEGV with a strlen error:
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- LSF recycles memory for C arrays, but sets a separate variable setting the size of the array to zero.
- JNA only sees the non-NULL pointer and starts to auto-access it, sometimes causing a SIGSEGV.
- In the short term neutered the jobInfoEnt structure so that this bad array is not autoRead().
QGraph updates:
- Job status is now checked in bulk every 30 seconds instead of one job at a time, even in the middle of dispatching jobs.
- If there is a hiccup (unexpected but not fatal error) during status check then the the error is ignored and status is checked again 30 seconds later.
- Jobs prefer to dispatch depth vs. breadth first.
More refactoring of SG framework separating the reusable code from the implementations.
The DistributedScatterFunction is still a work in progress and is not enabled yet. Still need to think through how Queue handles when a job dies.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5387 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 04:29:06 +00:00
60ddc08cdf
Added a boatload of new case-control association modules. Switched the U-test to use longs rather than ints (it just so happened that I overflowed and started getting negative U statistics. Not good.) Added the ALL association type for ease of specifying that we want to throw the book at something. Added an svn-commit.tmp~ because i can't get rid of it even with --force. Hopefully I can remove it after.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5386 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-06 21:58:12 +00:00
5c979633f0
Due to a problem in the way that dynamic type selection works, I've added an explicit (temporary) ability to restrict VE to specific variant types (SNPs, INDELs, etc), so that calculations will work when a site has a SNP in dbSNP but is called as an indel, causing the SNP site to mysteriously disappear from the comp track, a huge problem for validation report. VEU updated to allow both dynamic type (old) and just returning everything in the track.
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Also, created a standard Queue script that calculates a suite of standard indel and SNP assessment results. Will be the basis for a general evaluation Queue script with standardized data files for SNPs and Indels.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5385 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-06 19:31:12 +00:00
2f1e249aed
A proper validation report, calculating TP, FP, FN, sensitivity, FDR, PPV. Treats comp as a set of sites that have been either filtered (failed in assay), validated (polymorphic among samples), or invalidated (AC=0 or all genotypes = hom-ref). Very useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5384 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-06 19:27:40 +00:00
af71576a07
CalculateChromosomeCounts() now only calculates AC, AF, and AN when there are genotypes. Can now combine variants with headers that differ in only whether a field is a integer or a float. Updated CombineVariants integrationtest, as incorrect AC values where being calculated in the previous GS outputs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5383 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-06 19:25:52 +00:00
5b8fdc5b1f
Slightly optimized calculation for ~linear exact model, as well as totally incorrect banded calculation, for future development, if this proves useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5382 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-06 18:47:08 +00:00
fc5a071de2
Output format is 10^6 times better - now uses the multiplexer to write tdf tracks that can (after conversion to binary with igvtools) can be loaded directly into igv.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5381 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-06 18:23:52 +00:00
a40a8006b5
Added in unit tests for the statistics calculated by the test runner; and bug-fixes to the calculations; so we have some assurance that the statistics coming out the back-end are correct.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5380 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-06 16:54:02 +00:00
c40efe1dea
Fixed exception for BAMs without filenames (unit tests, BAM input streaming,
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etc.).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5379 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-06 13:43:49 +00:00
ad51f30244
A trivial, but useful, sum of a list of integers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5378 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-05 06:09:05 +00:00
9a8356892a
Cleaner error (really now just warnings) if you can't reach the S3 for logging
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5377 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-05 06:08:35 +00:00
10516f5de4
Fixed one low-memory sharder performance culprit: regions with no BAM data
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whatsoever were misusing the Picard MergingIterator, triggering a re-traversal
through the entire contig.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5376 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 21:26:22 +00:00
337b54136f
2 fixes. For Mark: when insertions can be partially left-aligned, we were reading off the wrong bases. For GS post: the stored VariantContext.REFERENCE_BASE_FOR_INDEL_KEY needs to be updated when left-aligning because it can change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5375 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 21:00:08 +00:00
b42005e7d7
Fixed issue where comp tracks with genotypes that didn't exactly overlap the eval track were getting dropped. Fixed issue where the 'row' column wasn't being output for things implementing TableType. This is an urgent patch for Mark - it'll break tests until I go back and update the md5s.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5374 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 16:51:12 +00:00
1861ca90fc
A change to the definition of CpG sites (is now, from 5' to 3' a CG dinucleotide in the reference, and the CpG site is at the C, rather than either at the C or a G).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5373 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 15:36:07 +00:00
9ca1dd5d62
Miscellaneous changes:
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- RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it)
- VCFUtils: grabbing VCF headers given a prefix
- MathUtils: Useful functions for calculating statistics on collections of Numbers
- VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure.
- Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored
in the window optionally different from those returned by whatever statistic is run across the window
Added:
- MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that
it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation
for when one of the sample sets is small, and the other large. Unit tests to follow.
- BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations
- BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-03 22:43:36 +00:00
8ae42b70ac
give it an annotated VCF and a BAM and it creates a truth table on the validation of the VCF calls. This is just the first version, not ready for primetime.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5371 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-03 21:45:11 +00:00
f7ef35b8f5
Removing untrue comments in the GaussianMixtureModel
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5369 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-03 18:18:47 +00:00
9e12cd1312
Gotta include the changes i made to get an init function into the contexts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5368 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-03 15:45:51 +00:00
835a26d145
A pass at a sample-normalized test. I think maybe all of them will simply do their own normalizing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5367 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-03 15:42:25 +00:00
ef38fd1e0e
Major refactoring of association testing framework. New modules are now beyond trivial to implement. One hurdle remains which is how to deal with statistics that ought to be sample-normalized (e.g. depth, insert-size [when multiple libraries are used], and possibly others).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5366 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-03 14:27:16 +00:00
5d4bbf41fb
Behave intelligently in the deepest levels of GATK record filtration when
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we find a read flagged as 'mapped' in the unmapped region at the end of the
file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5365 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-03 04:52:55 +00:00
7a22f19366
More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated
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case UserException.MalformedBAM to match case of UserExceptio.MissortedBAM for consistency and
ease-of-use.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5364 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-03 03:55:24 +00:00
0181d95fe4
Intermediate optimization checkin. LinearExact model now about 10-20% faster than previous commit, by reorganizing and optimizing the if statements and genotype likelihood calculations. Next commit will include a banded implementation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5362 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 22:01:35 +00:00
f0f4bc3363
This was busted because it assumed 1 (and only 1) record at each position. However it's possible to have 0 (which generated a NullPointer) or 2+ records (which dropped records).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5361 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 21:35:50 +00:00
c152ef4339
Better error message for unknown reference file extension.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5359 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 17:52:16 +00:00
bef83b8b09
Bug fix: was tracking state across BAMs that should've been tracked per-BAM.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5358 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 17:32:06 +00:00
bafa61c1fe
LINEAR_EXACT now the default model. Passes all integration tests. 2-3x faster in low-pass data. Tests on exome data ongoing, but potentially vastly faster there.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5357 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 17:14:36 +00:00
8e1aa6059a
New mode for CombineVariants to assume the incoming VCFs have the same samples and disjoint calls. Drastically reduces the runtime for routine combining operations. Very useful with Queue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5356 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 15:52:17 +00:00
5e4b321f86
Add hidden command-line argument for low-memory sharding.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5355 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 15:13:16 +00:00
ae42c0c7da
Bug fix based on GATK run report
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5354 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 14:18:12 +00:00
660998065b
'Okay, now I'm absolutely certain that there are no more bugs in the constrained writer.'
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5353 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 03:48:40 +00:00
880c607d79
Disable validation of linear index against original linear index process.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5352 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 01:51:26 +00:00
dc62685a2f
For Ryan: force creation of BAM index when no reads are present in the BAM
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file. Temporary fix until Picard changes the behavior of indexing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5351 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 01:50:42 +00:00
570186fa42
Added (deep) clone() and merge() to the RunningAverage utility class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5350 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 00:35:23 +00:00
43567b7fe3
Load the linear index without forcing the index for the entire contig to be
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loaded into memory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5349 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 00:08:39 +00:00
a20ce1436d
A temporary @hidden hack to get indel calling done for Phase I: don't try to call if there's too much coverage. Do not use this unless your last name rhymes with Shmoplin.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5348 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-01 19:22:27 +00:00
3c7ae0d1a6
Special case handling of unmapped region in low memory sharder.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5346 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-01 17:38:30 +00:00
dd30ad751a
Fix bug in low memory sharder's interval accumulator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5345 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-01 17:11:22 +00:00
d6145de970
More comprehensive tracking of position when bin trees are sparse.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5344 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-01 15:53:43 +00:00
bb969cd3a2
EMIT_ALL_SITES now does exactly that - even when there's no coverage or too many deletions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5343 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-01 05:05:00 +00:00
0723b0f44c
Generalized association is now working. Output is in a horrific format. Implementation of T-testing. Improvements are to look for classes dynamically (a la VariantEval/VariantAnnotator), beautify output, and do optimizations where they exist.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5341 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-01 01:23:37 +00:00
ce34a8a918
New hidden option in VQSR to not parse the genotypes of the incoming training data. Updated VQSR training in methods development pipeline to be more in line with best practices.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5340 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 23:19:51 +00:00
e7089f9870
Fix for particularly small, isolated intervals: make sure the bounds of the
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bin tree are dictated by the lowest bin level, whether it exists or not.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5339 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 22:35:53 +00:00
c869d1c9cf
Fix misc issues in new protosharder regarding proper iterator termination when
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an unexpectedly small amount of data is present.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5338 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 21:14:18 +00:00
5ac9af472c
Adding performance test for case with very high coverage (> 600,000x) over an interval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5336 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 19:48:56 +00:00
e75366f738
Fixed performance issue in protosharding code -- turns out that the index
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optimizer was mutating the data stored in the indices. Protosharding still
disabled by default.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5334 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 17:32:12 +00:00
8de83725f9
Simple walker to randomly break VCF files into (potentially unequal) subsets. Useful for e.g. cutting hapmap into training and evaluation sets.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5333 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 16:51:46 +00:00
d059d89a9d
Fixes and cleanups for indel eval module. Also outputs AT/CG ratio in dedicated column in IndelStatistics.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5332 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 12:07:50 +00:00
05fac8583d
Following up Mark's recent commit: hooking up the --maxPositionalMoveAllowed argument into the indel realigner and through to the SAM writer. We now ensure that no read is realigned more than N bases (200 by default, which is nowhere close to realistically possible). If anyone ever sees a warning message about this with the default value then please let me know because I need to see it for myself.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5331 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 04:40:54 +00:00
874406352c
Accidentally commited the N2 comparing test as well...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5330 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 04:15:30 +00:00
1dedfdb11b
Fixes for constrained movement Indel Realigner. Now sorts all of the reads in the interval before handing them to ConstrainedMateFixingSAMFileWriter to maintain correct contract between the two pieces of software
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5329 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 03:52:18 +00:00
d216830b92
Experimental linear version of the exact model. In testing, but gives identical results to N2 gold standard version, and passes integration tests. Performance optimizations still ongoing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5328 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 03:48:11 +00:00
54facb2c51
Small change for Mauricio so that the correct metrics get output when running in GENOTYPE_GIVEN_ALLELES mode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5327 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-27 06:08:32 +00:00
7ff8d23c64
Don't do genotype concordance on comp tracks without genotypes, even if they have an AC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5321 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-25 21:11:50 +00:00
600f73cbd6
A checkpoint commit of two BAM reading projects going on simultaneously. These two projects
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are works in progress, and this checkin will provide a baseline against which to gauge
improvements to both projects.
Low-memory BAM protoshards (disabled by default):
- Currently passing ValidatingPileupIntegrationTest.
- Gets progressively slower throughout the traversal, but should run at least as fast as original implementation.
- Uses 10+ file handles per BAM, but should use 3.
BAM performance microbenchmark test system:
- Currently tests performance of BAM reading using SAM-JDK vs. GATK
- Tests do not hit all GATK performance hotspots.
- New tests that require input data in a slightly different form are hard to implement.
- Output of test results is not easily parseable (investigating Google Caliper for possible improvements).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5317 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-25 17:50:32 +00:00
5d28cbda27
When crossing contigs it's crucial that the queue get flushed or else it will continue to accumulate reads without emitting. This is the last time I trust someone when they tell me that they are 'confident there are no bugs' in a tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5315 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-25 05:18:30 +00:00
cba88a8861
Elegant solution to the determinism problem: force testNG to run tests in the order that I want it to.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5312 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 21:32:35 +00:00
1129f1535d
Fix for the HaplotypeScore optimization in AlignmentUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5310 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 20:40:18 +00:00
15dfac6bf7
Updating integration test to be in sync with previous commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5309 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 20:21:58 +00:00
06e3c34e7f
Updating performance test to be in sync with previous commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5308 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 20:13:35 +00:00
0f1c1fa26f
First general association module. Let the bug fixing begin!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5307 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 19:55:33 +00:00
292b421113
Framework for generalized association testing. Heavy lifting done in implementation of the AssociationContext(s) and AssociationContextAtom(s). Nothing really implemented.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5306 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 18:12:39 +00:00
2f2aa339d9
Now makes all pairs, not only the good ones. The logic of selecting the "best" pair when the data are messy (e.g. multiple alignments available for an end) is still very naive
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5303 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 16:21:26 +00:00
abf3fcbb72
Little changes in recognized annotation terms; columns in annotated maf are now prioritized and multiple alternatives do not cause 'i don't know what to do' crash: e.g. if Chromosome and chr columns are both present, then Chromosome is taken (has a priority).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5302 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 16:19:06 +00:00
255cc246a2
Change in Methods development pipeline: dbsnp130 can't be used for anything, changed it to dbsnp129. Optimization for HaplotypeScore and the to-be-committed ReadRosRankSumTest in AlignmentUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5301 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 16:09:03 +00:00
97e1a5262e
-ct x no longer includes coverage in the previous bin
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BatchMerge - additional support for indels (can't just test the alternate allele when it's an extended event, must also specify that you want to use the dindel model when you actually test the allele)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5300 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 15:52:04 +00:00
ee6f112556
Phase 3: constrained movement is now the only option available in the realigner (so I guess technically it's not really an option). Several command-line options are deprecated. Code cleaned up. Wiki updated. Release coming. One phase left...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5299 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 14:59:48 +00:00
93888e570b
Phase 2: after hours of testing, confirming that constrained mode looks good so moving the integration tests over to use it. Some cleanup. More cleanup coming in Phase 3.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5298 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 06:23:41 +00:00
c59c8b9872
Phase I of my promise to Mark: fleshed out integration tests for Indel Realigner
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5297 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-23 21:05:20 +00:00
75bd0129e7
quick bug fix.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5296 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-23 19:16:20 +00:00
9357bee921
Don't skip tri-allelic alleles passed in - just choose the first one.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5293 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-23 17:25:50 +00:00
a2301383bb
quick walker to find out where the reads mapped to huref were mapped in the consensus reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5292 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-23 17:00:17 +00:00
318035c147
Fixing up the output system of the Unified Genotyper. Deprecating the -all_bases and -genotype arguments. Adding instead the --output_mode (EMIT_VARIANTS_ONLY, EMIT_ALL_CONFIDENT_SITES, EMIT_ALL_SITES) and --genotyping_mode (DISCOVERY, GENOTYPE_GIVEN_ALLELES) arguments. UG now does the correct thing when passed alleles (bound to the 'alleles' rod) to use for genotyping; added several integration tests to cover this case. This commit will break the batched calls merging script, but Chris knows this and is ready for it...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5288 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-22 06:07:18 +00:00
d7f98ccd9c
Adding --doNotWriteOriginalQuals argument to BQ recalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5286 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-22 04:00:00 +00:00
1a5d296737
ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5284 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-21 14:02:41 +00:00
aa4a4e515d
Safer interface for ReorderSam. Better error checking. Documentation. Moving into Picard now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5283 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-20 14:35:44 +00:00
cd7a7091ba
Lexicographic error points users to the ReorderSam wiki entry
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5281 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-19 23:45:37 +00:00
444bf83acf
A simple utility for reordering a BAM file based on a new reference sequence. This tool can be used to efficiently correct a lexicographically sorted BAM file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5279 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-19 23:24:32 +00:00
290afae047
GSA-423 Better reporting for errors in QScript.script().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5276 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-18 22:21:15 +00:00
52f860c9b2
Modified MD5s to account for Andrey's new MNP column in CountVariants.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5274 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-18 13:13:58 +00:00
cb95e68fc0
CpG is no longer a standard stratification.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5273 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-18 07:17:35 +00:00
9ddee96f93
When subsetting by sample, need to take extra care that hom-ref sites don't accidentally get treated as variant sites in CompOverlap. Renamed convenience method for creating command-lines in integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5272 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-18 06:26:38 +00:00
1bc5c7e99b
boneheaded mistake, mixed up my min and max
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5271 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-18 04:02:14 +00:00
92c82200c9
Fixed an issue where an eval module with TableType objects would get an extra, empty table in the output, screwing up the parse in R.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5267 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 23:03:46 +00:00
7ffcade3c3
Added MNP to recognized and counted event types
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5266 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 22:37:38 +00:00
57c66b5602
Supports GQ now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5265 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 22:30:25 +00:00
a189454343
FCP only adds the expand intervals QFunction once per script instead of once per QFunction using the ExpandTargets scala trait.
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Eval dbSNP's type now based on eval dbSNP instead of genotype dbSNP.
Using an external treemap instead of the JGraphT internal node set to speed up larger graph generation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5261 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 19:09:03 +00:00
f1d708f4d4
Fixes for HRun annotation in case of indels:
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a) In case of a deletion value was completely broken, we'd report 0 or -1.
b) For indels, we report maximum of forward and backward values - I've seen empirically many sites which are not strand biased but which seem to be artifacts and the homopolymer run is always to the right only (because we left align by convention).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5260 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 18:57:21 +00:00
0e04e95245
Bug fix: when extracting reference sequence for the event from the reference genome, the tool was treating Deletions and MNPs of length N in exactly the same way: ref_bases[current_pos+1,...,current_pos+N]. This is correct for Deletions but not for MNPs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5258 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 16:15:42 +00:00
52eedaf22d
Subtle but very annoying bug due to incorrect exit condition on backward traversal. Example of incorrect old behavior (found by Martha Borkan, this normally would NOT happen with the combination of match/mismatch/open/extend parameters we have been using; use match=10.0, mismatch= -9.0, open= -15.0, extend= -6.66 in older builds in order to reproduce):
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let's align two sequences (shown below, good alignment)
AAATTTGGTAAAA-GT
AAATTTGGTAAAAGGT
now let's reverse the same very sequences and align again
TGAAAATGGTTTAAA
TGGAAAATGGTTTAAA
Note how we lost the deletion and got a mismatch instead at the very first letter of the upper sequence. The overall score of any particular alignment does not depend on the direction of the traversal, so the best alignment (with the highest score) should stay the same too.
New version fixes this issue and produces correct alignment of reverse sequences (up to the different choice of redundant position for the deletion):
T-GAAAATGGTTTAAA
TGGAAAATGGTTTAAA
This version also has the main() method reinstated, so the aligner can be run on its own as a little app.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5255 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 00:02:32 +00:00
6e291820d3
GeneNamesIntervalWalker outputs all genes in each interval; walkers now require a ROD named "intervals"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5254 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-16 19:58:09 +00:00
b304ced801
Updated haplotype calculator to correctly terminate haploptypes RIGHT BEFORE an unphased het
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5252 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-16 17:10:01 +00:00
5a51c9a815
AWS_S3 logging is now enabled by default. It first tries to log internally at the Broad, and if it can't goes to AWS_S3. DEV option is removed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5249 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 20:20:14 +00:00
d185c2961f
Added pipeline for calling FCP in batches called MultiFullCallingPipeline.
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Bug smashes for the MCFP:
Synchronized access to LSF library and modifications to the QGraph.
If values are missing from the graph with -run make sure to exit with a non-zero.
Refactored QGraph to pre-generate a unique Int for each QNode speeding up getHashCode/equals inside the graph.
Added jobPriority and removed jobLimitSeconds from QFunction.
All scatter gather is by default in a single sub directory queueScatterGather.
Moved some FCPTest into BaseTest/PipelineTest for use by MFCPTest.
Rev'ed the 1000G bams used for validation from v1 to v2 and added code to look for the bams before running other tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5247 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 18:26:14 +00:00
d6e3f2eba6
Added GC content calculator for CNV data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5240 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-14 22:29:55 +00:00
7a11b4f35d
Another change in variant classification values
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5237 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-14 17:47:58 +00:00
7f7d7eb2d1
Inconsequential changes, more 'variant classification' values are recognized
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5236 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-14 17:36:39 +00:00
d3660aa00e
Very basic functionality for annotating indels (specifies whether the indel is frameshift, inframe, or non-coding). Does not attempt to recalculate the variant codon, variant amino acid, or whether the site falls within a splice region. Added a convenience method to WalkerTest for building command-line arguments with the proper spacing (so that I stop getting annoyed when I've gotten it wrong and the test system yells at me.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5235 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-13 17:58:20 +00:00
8d6db5d188
Additional logging of the temp file creation, management, and merging process
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for VCF files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5234 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 22:07:25 +00:00
03482bf7c4
Number of MQ0 reads in each sample (format field)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5229 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 17:16:26 +00:00
8560bb290b
Allelic fractions are now computed on MQ>0 reads only; total depth in each sample still includes MQ0 as per usual convention. Also renamed for clarity.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5228 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 17:13:15 +00:00
9554df1a7c
Adding integration test for indels in VF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5227 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 16:58:57 +00:00
b992abb6eb
A few more unit tests plus some extra
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functionality for BAM index visualization.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5222 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-09 01:51:34 +00:00
4d1cca95bb
Removed deprecated getDbsnpFile.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5221 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 21:12:15 +00:00
a8ab5a5fb9
After code review with APSG, trying a patch for SIGSEGV errors which checks the LSF result codes from lsb_openjobinfo instead of checking for a null return value from lsb_readjobinfo.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5220 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 21:08:22 +00:00
f3de9ee3e0
Refactoring of indel evaluation code to make it easier for external functions to get access to indel classification, in preparation for IndelMetricsByAC to stratify indel classes by AC (not done yet).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5219 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 17:35:16 +00:00
3635606cd8
Temp checkin just for experimentation: exposed probabilistic alignment parameters to command line interface to make it easier to experiment on their effects, although a full scrap/rewrite of this should be coming soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5218 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 17:33:29 +00:00
196eb77699
CG var format is screwed up and doesn't quite fit into the VariantsToVCF mold (we need to see multiple records before we can assign genotypes to a given position), so it's safer to keep this separate from the other well-behaved formats. Hopefully, it's temporary anyways.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5216 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 03:18:38 +00:00
4fe0fcd707
Updates to handle CG data, headers, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5215 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 03:16:05 +00:00
8040998c15
Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp.
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Added a genotypeDbsnpType and evalDbsnpType to check the extensions for .vcf or .rod.
Moved renaming of "recalibrated" bams to "cleaned" from sed to yaml generation template (see diff for more info).
Renamed fCP.q to FCP.q.
Though it's still disabled until VariantEval is updated, added changes above to the FCPTest.
Removed refseq table from the queue.sh wrapper script. Only specified in the yaml.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5213 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 22:01:09 +00:00
bceb2a9460
Now that Mauricio has updated the PacBio BAM to properly have RG, can use sample name in the walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5212 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 20:26:57 +00:00
ecbc38aff0
If no comp rod is specified, specify the dummy name none so that we still get counts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5211 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 19:24:52 +00:00
1fbfd4082e
Cycle covariate now works with pacbio reads. No need to override the platform anymore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5210 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 17:14:55 +00:00
2a04e0d378
Explicitly set logger's level to info - otherwise samtools is too chatty
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5209 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 17:08:50 +00:00
698096dc5a
Moving VariantsToVCF to the proper directory; removing the oneoffs CG indel converter in preparation for a ligitimate CG variant Feature class in the works.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5207 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 05:21:01 +00:00
35c688ac67
Updated md5 for testVCFStreamingChain to reflect latest changes to VariantEval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5206 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 21:22:05 +00:00
1f820d5026
Added two files from some refactoring changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5205 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 19:20:12 +00:00
1085bbf303
Fixed issue where all comp tracks were being treated as known tracks. Fixed issue where multiple JEXL expressions were causing an exception because the underlying object did not implement the Comparable interface. Fixed issue where variants being compared to the known track were not being checked for equality of variation type. Fixed issue where functional annotations were not being iterated over properly. Refactored a lot of helper methods into a separate VariantEvalUtils utility class. Significantly expanded the test suite using a small VCF with SNPs, indels, and non-variant loci which makes it much easier to see what the proper answer should be, and included the appropriate grep and awk commands in the comments to confirm the values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5204 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 19:19:20 +00:00
cc5d695bcf
Renamed the IPFL Test to IPFL PipelineTest so that it'll be picked up by the PipelineTests.
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HACK: Turned off JNA autoRead() in the jobInfoEnt LSF structure to try and dodge the SIGSEGV during strlen calls during bmods.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5201 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-05 00:06:12 +00:00
ce51ffb56e
Oops, old local paths committed on accident.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5200 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 23:35:56 +00:00
29f3ad72f3
SAMFileWriter that allows the user to move reads, but only a bit, in an incoming coordinated sorted BAM files. Does some local reordering and local mate fixing, under specified constrained. These constrains allow us to make a special -- under testing for Eric, who promised to try this out a bit, expand test cases and integration tests -- but soon to be the default and only model of the realigner that only moves reads with ISIZE < 3000 that directly emits a coordinate sorted, mate fixed validating BAM file without needing FixMates externally. Preliminary testing shows this runs in a totally fine amount of memory and produces equivalent results to the previous version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5199 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:27:05 +00:00
11ea321b39
Trivial header cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5198 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:23:15 +00:00
fe4aa58d35
Removing unused class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5197 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:22:28 +00:00
0ad1ea4aa1
Fixed Umapped misspelling
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5196 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:21:41 +00:00
03f265d8bd
Change DP format field description in the header line (expected count=1)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5195 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 21:28:25 +00:00
c0e998621c
Computes two format (genotype) level annotations: total read depth in the given sample (DP format field) and fraction of reads supporting alt allele(s) in the given sample (FA format field)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5193 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 21:23:55 +00:00
8700b74640
Now annotates indels as well. Probably can also annotate mixed vcf with indels +snps, but not tested in that mode...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5192 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 20:28:03 +00:00
5c3198520c
A few minor modifications masquerading as significant changes according to
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svn's logs:
- Copied BAM indexing engine from Picard back into the GATK anticipating
shard merging algorithm. Tried to leave most of the building blocks in
Picard. If this turns into a logistical nightmare, I'll merge the building
blocks into the GATK as well.
- Reorganized the org.broadinstitute.sting.gatk.datasources package, giving
better separation of query and management functionality for reads, ref, rmd,
and samples.
- Merged Shard building blocks into org.broadinstitute.sting.gatk.datasources.
reads package, indicating it's current strong relationship with the reads,
rather than the general unifying element I wish this would be.
- Collapsed BAMFormatAwareShard into Shard.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5184 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 17:59:19 +00:00
9ddc95c833
NewEvaluationContext needs to be generated in the inner loop. Otherwise, multiple comp tracks end up getting routed to the same row of the output table. Added test to cover multiple comp tracks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5181 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 07:04:53 +00:00
918cc09477
Allow multiple records at a position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5178 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 04:19:05 +00:00
cb6454bf98
Multiple eval tracks should be bound with different names, rather than just 'eval'. Added tests to cover usage with multiple tracks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5177 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 22:33:50 +00:00
5a8e2c2739
Going through the backlog of emergency hacks I put in for the 1000G release. It is possible to call a site in an analysis panel but when using all samples the site isn't called because of going over the minimum deletion threshold, for example.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5174 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 15:12:26 +00:00
3839fd1a25
Updated phasing pipeline to properly read samples from VCF and BAM files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5172 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 07:16:05 +00:00
43fb11b923
Removing stray non-ASCII character
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5171 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 03:10:08 +00:00
2732c839d4
Restored parallelism and associated tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5170 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 02:04:03 +00:00
fd8dd8fb9b
Fixed an issue where a no-call in the eval track would prevent a site from a comparison track from being loaded. Added a new test to cover the use case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5169 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 01:47:53 +00:00
798955b006
After discussing with Mark, revert to "Master merging" of phase information from VCFs. This has the advantage of creating minimal phased VCFs from RBP, from which phase info is merged into the original "master VCF". Also, updated Genotype.sameGenotype() to be simpler and NOT REVERSE the ignorePhase flag in comparing Allele lists/sets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5167 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 19:50:15 +00:00
dac83d21bc
Fixes for IndelLengthHistogram for someone on GS. This evaluator apparently doesn't have an integration test. I'll fix that tonight.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5166 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 19:48:09 +00:00
06b63d8336
Pulled out CpG stratification in test results at Kiran's suggestion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5165 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 18:36:09 +00:00
25f045cac6
Changing locking errors to warnings. This will hopefully allow us to diagnose
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the mysterious failure in STING_INTEGRATION-3832, the next time it appears.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5164 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 16:29:31 +00:00
91297c138b
Update VCFStreamingIntegrationTest to use new variant eval command-line
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arguments, output format.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5162 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:40:43 +00:00
7d89ce820b
Got tired of waiting for Kiran to fix the build: updated NewVariantEval ->
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VariantEval.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5161 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:32:39 +00:00
96241c6637
More testng fallout: fixing another seemingly 'random' issue arising from an
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alternate test ordering.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5160 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:25:50 +00:00
e5e65ecfbe
Bugfix for GetSatisfaction: ensure that the two statistics objects (the map, and the pair) are actually pointers to the very same object.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5156 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 06:40:42 +00:00
34f5587f2c
As with the cleaner, don't exception out when trying to get the GATK version after -Ddisable.help=true
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5155 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 06:08:59 +00:00
4243f0dea7
1) Fix for Tim et al: HashMaps don't necessarily return objects in a deterministic fashion when keys are pointers; break it apart into a list.
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2) Fix for Kiran: when running with -Ddisable.help=true, don't exception out when trying to get the GATK version.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5154 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 06:06:48 +00:00
e74f28ad89
If there's an LSF queue maximum time limit set and the user hasn't specified one for this job, pass on the queue defined maximum limit with the job.
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Updated LibBatIntegrationTest to use proper networked temp directory accessible by local machines and nodes.
Disabling the FCPTest until the VE3 is incorporated into the fullCallingPipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5151 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 23:13:09 +00:00
391f248640
Inserted a dangerous (but hidden) command-line argument for use by the Picard team.
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Used to process intervals over BAMs without indices. Tim understands the risks but
wants this anyway, as a temporary solution to a pipeline problem.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5148 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 22:10:06 +00:00
4cb910bc38
Fixed import statements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5145 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 19:26:37 +00:00
d4f744a4d4
Checking if the interval files exist before using them to calculate the minimum scatter parts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5143 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 18:07:34 +00:00
b7aac3b846
Corrected import statement to reflect VE3's new position in core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5142 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 18:01:02 +00:00
3f387bc8d8
Transitioned over to VE3 architecture.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5141 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 17:54:18 +00:00
401feca90d
Updates to VariantEval 3.0 integration test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5140 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 17:45:06 +00:00
cab426f86f
VariantEval 3.0 is now in core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5139 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 17:42:08 +00:00
c59b2a8296
Removed experimental "master merging" from CombineVariants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5138 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 17:13:05 +00:00
b0432ee1e2
First part of a two-stage commit. Removing old VariantEval to make room for VariantEval 3.0 in core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5137 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 17:03:41 +00:00
d406d9b3fc
There's no reason to special case no-calls if they already have PLs associated with them. Just use the PLs!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5136 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 15:05:45 +00:00
83dcca7e82
Added ability to load a GATKReport from disk.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5134 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 05:31:49 +00:00
5e7a5cf924
Quick fix for Danny Lieber: flesh out the additional functionality required
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to align to a reference other than what's specified in the header.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5133 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 05:28:37 +00:00
b5d1aab8dc
Scripts to create the GATK IAM user and give him/her rights to PutObject (and only PutObject) into the S3 storage instance. Updated the GATKRunReport to now upload using the GATK user, not mark@depristo.com. Running with -et AWS_S3 sends run reports up to the Amazon S3 cloud now. Going to request a few external users try this option so we can see it running at scale. I'm sure S3 can handle a few hundred thousand 1Kb uploads per days, though
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5132 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 03:48:33 +00:00
e26da9b047
Changed column-key names to not have spaces, as GATKReport gets very upset about this.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5131 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 03:31:54 +00:00
197c91e2fb
Working implementation of GATKRunReport POSTing to Amazon Web Services S3 storage. Requires users to explicitly provide the secret key to do the upload. Am investigating options to avoid having to do this in the future. Pretty cool little experiment for those who are interested in S3 interaction (extremely trivial)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5130 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-30 21:23:54 +00:00
8640ca6278
Trivial bug fix so that we don't bring the start up TraversalEngine banner twice when we only process a single locus
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5129 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-30 21:22:16 +00:00
2ef66af903
Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high.
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Moved the BamListWriter from FCP to ListWriterFunction in the Queue core.
Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s.
Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 23:33:58 +00:00
04d66a7d0d
Updated integration test's MD5s reflect the fact that assay sequences were previously designed incorrectly for indels, the bug is now fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5120 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 23:00:22 +00:00
5934b9cb82
Augment function isChrM by allowing "CRS" in addition to "chrM" or "MT", as a standard contig name indicating the mitochondrial chromosome. CRS stands for Cambridge Reference Sequence and is the standard in the field.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5119 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 22:45:45 +00:00
depristo
rpoplin
fromer
droazen
kshakir
asivache
carneiro
hanna
chartl
corin
delangel
ebanks
kiran
scalvo