866f4fd569
Test version of consensus compressing strategy. Cannot be used, and is being rewritten right now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5605 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 18:37:03 +00:00
80d547ae71
Fix for bug GSA-445: Sequence dictionary validation can be very slow with
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large numbers of contigs. SequenceDictionaryUtils.getCommonContigsByName() was
running in O(n^2) time due to poor choice of data structure -- modified it to
run in O(n) time. Also removed an unnecessary O(n log n) step at another stage
in the sequence dictionary validation process. In tests with a 181,813-entry
sequence dictionary, runtime improved from an average of 21.4 minutes to 45.1
seconds.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5604 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 18:33:10 +00:00
b6e7b5dace
Updating to reflect my recent Tribble fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5601 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 11:48:00 +00:00
4f17004590
Allow walkers to enforce the ordering in which ReadFilters are applied (so that they're now done in the order specified in the walker). Useful if you have a computationally expensive filter (like adaptor clipping) that should only be applied to reads passing all other filters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5600 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 03:34:50 +00:00
53db7b8faa
Did some refactoring which broke some unit tests, and then failed to run
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the unit tests. Definitely not my best effort...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5599 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 03:31:52 +00:00
74755cfd1c
Adding a ReadFilter to hard-clip out bases from adaptor sequences. This is actually slightly more correct than having it be part of LocusIteratorByState because it allows us to remove reads that are complete garbage (and there are definitely some) based on the insert sizes. However, although conceptually this is great, it doesn't actually work. 'Why?' you may ask. Because when we hard-clip reads it often changes their start positions... which means that reads are no longer passed to LocusIteratorByState in coordinate order... which makes it (understandably) barf all over the place (and makes for some really fascinating SNP calls). This took me forever to find. I'm going to bed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5598 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 03:15:58 +00:00
cd61ef7169
Re-enabling multi-threaded integration tests. To make this work, downsampling and annotations are disabled for this test so that we don't have randomization issues for it based on which shards get executed first.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5597 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 03:07:39 +00:00
fece2167b3
Prototype implementation of protoshard merging when protoshard n and protoshard
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n+1 completely overlap. Gives a small but consistent performance increase in
non-intervaled whole exome traversals (2.79min original, 2.69min revised).
Needs a more in depth analysis of optimal shard sizing to determine a true
optimum.
Also renamed a variable because Khalid disapproved of my naming choices.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5595 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 02:09:14 +00:00
32d502c122
Enable BAM OTF index writing by default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5594 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-07 23:44:25 +00:00
cb3e8aec5e
Modified the buildfile and help extractor doclet so that help text is only
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extracted from source files that have been modified since the help resource
file was last generated. This significantly speeds up builds where only a few
source files have been modified, at the expense of making clean builds take
slightly longer. Here's some performance data gathered by testing the old and
new versions of extracthelp in isolation and averaging across 10 runs:
old extracthelp, 1 modified source file: 20.1 seconds
new extracthelp, 1 modified source file: 7.2 seconds <-- woohoo! :)
old extracthelp, clean build: 17.8 seconds
new extracthelp, clean build: 20.5 seconds
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5590 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-07 18:40:53 +00:00
af09170167
As I threatened yesterday, I've moved the various and disparate randomization code out of the walkers. Now they all (except VQSRv1, whose days are numbered anyways) use a static generator available in the engine itself. Please use this from now on. The seed is reset before every individual integration test is run. I think there may still be an issue with the IndelRealigner but I need to confirm with the commit to see what testNG does. Integration tests are already broken anyways, so no big deal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5589 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-07 17:03:48 +00:00
45ebbf725c
Instead of always merging Picard interval files they are optionally merged by Sting Utils.
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Disabled the MFCP while the FCP gets an update.
Minor updates to email messages for upcoming scala 2.9.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5588 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 21:12:05 +00:00
89bb21d024
typo in the argument description
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5587 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 19:45:32 +00:00
3f3f35dea0
UnifiedGenotyper now BAQs via ADD_TAG to facilitate using BAQed quals for GL calculations but unBAQed quals for annotation calculations. UnifiedGenotyper now produces SNP and indel calls simultaneously. 40 base mismatch intrinsic filter removed from UG to greatly simplify the code. RankSumTests are now standard annotations but the integration tests are commented out pending changes that will allow random annotations to work.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5585 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 19:06:24 +00:00
1aa4083352
Fortunately this code isn't used by anyone right now, but it needs to be fixed before someone unwitingly does: flags were wrong according to the SAM spec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5584 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 17:16:41 +00:00
b231a40da5
Augment PrintLocusContextWalker with extended event info.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5583 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 13:42:48 +00:00
ab5c4064ed
quick bug fix for variant context utils: only calculate the max AC if we're using the mergeInfoWithMaxAC flag, and if so deal with sites that have multiple alternate alleles correctly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5582 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 05:36:52 +00:00
cc713f2769
fixing exception text
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5581 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 00:29:13 +00:00
4b451314b2
Only store a read in the mate hash if it could possibly be moved. This reduces memory consumption especially when dealing with a case of tons of unmapped reads at the end of the bam; however, it's only mildly helpful for chr1 of the Papuans (there's a truly massive pileup 120Mb into it; more thought needed at a later point). Integration tests changed only because some of the reads in the original bam were busted to begin with (it's an old pilot 1000G bam).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5580 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 22:20:09 +00:00
79b5fa6cc5
Structural refactoring in advance of dichotomization statistics; generalization of statistical test infrastructure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5579 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 18:52:32 +00:00
77ca4eef31
IntelliJ complains that @Override is not allowed when implementing interface methods. Whatever.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5578 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 16:57:59 +00:00
f4c06bb4ce
Traversal now says 'done with mapped reads' instead of 'done' so we don't confuse users when there are a lot of unmapped reads left to process.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5577 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 15:11:28 +00:00
5eccc7e528
Added annotation of INCORRECT SNP-based aa annotations in case of MNPdependentAA:true
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5576 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 02:46:45 +00:00
bb6a30611c
Forgot to modify the test too. What a bad commit. Sorry guys.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5575 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 02:11:08 +00:00
a0d096c993
Forgot an import statement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5574 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 22:55:00 +00:00
b52c3e7e30
Make the window and slide-by values command-line accessible, and standardize for every context. Move the test classes (which are abstract association context modules) into the proper directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5573 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 22:37:12 +00:00
db9908ec02
Small correction to the unit test code from my last commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5572 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 18:55:38 +00:00
a5acb0b7a6
Fix for bug GSA-314: Detect -XL and -L incompatibility. An ArgumentException is
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now thrown if the combination of -L and -XL intervals specified on the command
line results in an empty interval set after set subtraction.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5571 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 18:41:55 +00:00
b722ebf244
quick help/comments updates to match the wikipage.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5569 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 12:55:55 +00:00
96f0f0d706
Fixing use of String != String
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5568 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 01:12:00 +00:00
095125152b
Updated to now longer include 2nd-best base output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5567 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-03 20:13:10 +00:00
b2a0331e2d
Pushing hard coded arguments into VariantRecalibratorArgumentCollection
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5566 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-03 19:55:09 +00:00
79c43845ad
Changing Uniform approximation to Normal approximation in rank sum test. n factorial was overflowing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5565 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-03 18:18:39 +00:00
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
depristo
droazen
ebanks
hanna
kshakir
carneiro
rpoplin
aaron
chartl
asivache
fromer