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Author SHA1 Message Date
depristo 5b8fdc5b1f Slightly optimized calculation for ~linear exact model, as well as totally incorrect banded calculation, for future development, if this proves useful. 
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
chartl 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. 
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
chartl 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. 
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
hanna c40efe1dea Fixed exception for BAMs without filenames (unit tests, BAM input streaming, 
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
depristo ad51f30244 A trivial, but useful, sum of a list of integers 
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
depristo 9a8356892a Cleaner error (really now just warnings) if you can't reach the S3 for logging 
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
hanna 10516f5de4 Fixed one low-memory sharder performance culprit: regions with no BAM data 
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
ebanks 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. 
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
kiran 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. 
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
kiran 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). 
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
chartl 9ca1dd5d62 Miscellaneous changes: 
- 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
carneiro 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. 
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
rpoplin f7ef35b8f5 Removing untrue comments in the GaussianMixtureModel 
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
chartl 9e12cd1312 Gotta include the changes i made to get an init function into the contexts 
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
chartl 835a26d145 A pass at a sample-normalized test. I think maybe all of them will simply do their own normalizing. 
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
chartl 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). 
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
hanna 5d4bbf41fb Behave intelligently in the deepest levels of GATK record filtration when 
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
hanna 7a22f19366 More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated 
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
depristo 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. 
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
ebanks 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). 
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
depristo c152ef4339 Better error message for unknown reference file extension. 
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
hanna bef83b8b09 Bug fix: was tracking state across BAMs that should've been tracked per-BAM. 
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
depristo 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. 
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
rpoplin 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. 
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
hanna 5e4b321f86 Add hidden command-line argument for low-memory sharding. 
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
ebanks ae42c0c7da Bug fix based on GATK run report 
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
ebanks 660998065b 'Okay, now I'm absolutely certain that there are no more bugs in the constrained writer.' 
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
hanna 880c607d79 Disable validation of linear index against original linear index process. 
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
hanna dc62685a2f For Ryan: force creation of BAM index when no reads are present in the BAM 
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
asivache 570186fa42 Added (deep) clone() and merge() to the RunningAverage utility class 
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
hanna 43567b7fe3 Load the linear index without forcing the index for the entire contig to be 
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
ebanks 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. 
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
hanna 3c7ae0d1a6 Special case handling of unmapped region in low memory sharder. 
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
hanna dd30ad751a Fix bug in low memory sharder's interval accumulator. 
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
hanna d6145de970 More comprehensive tracking of position when bin trees are sparse. 
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
ebanks bb969cd3a2 EMIT_ALL_SITES now does exactly that - even when there's no coverage or too many deletions 
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
chartl 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. 
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
rpoplin 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. 
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
hanna e7089f9870 Fix for particularly small, isolated intervals: make sure the bounds of the 
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
hanna c869d1c9cf Fix misc issues in new protosharder regarding proper iterator termination when 
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
ebanks 5ac9af472c Adding performance test for case with very high coverage (> 600,000x) over an interval 
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
hanna e75366f738 Fixed performance issue in protosharding code -- turns out that the index 
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
ebanks 8de83725f9 Simple walker to randomly break VCF files into (potentially unequal) subsets. Useful for e.g. cutting hapmap into training and evaluation sets. 
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
delangel d059d89a9d Fixes and cleanups for indel eval module. Also outputs AT/CG ratio in dedicated column in IndelStatistics. 
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
ebanks 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. 
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
depristo 874406352c Accidentally commited the N2 comparing test as well... 
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
depristo 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 
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
depristo 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. 
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
ebanks 54facb2c51 Small change for Mauricio so that the correct metrics get output when running in GENOTYPE_GIVEN_ALLELES mode. 
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
depristo 7ff8d23c64 Don't do genotype concordance on comp tracks without genotypes, even if they have an AC 
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
hanna 600f73cbd6 A checkpoint commit of two BAM reading projects going on simultaneously. These two projects 
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
ebanks 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. 
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
ebanks cba88a8861 Elegant solution to the determinism problem: force testNG to run tests in the order that I want it to. 
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
rpoplin 1129f1535d Fix for the HaplotypeScore optimization in AlignmentUtils 
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
ebanks 15dfac6bf7 Updating integration test to be in sync with previous commit 
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
ebanks 06e3c34e7f Updating performance test to be in sync with previous commit 
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
chartl 0f1c1fa26f First general association module. Let the bug fixing begin! 
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
chartl 292b421113 Framework for generalized association testing. Heavy lifting done in implementation of the AssociationContext(s) and AssociationContextAtom(s). Nothing really implemented. 
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
asivache 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 
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
asivache 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). 
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
rpoplin 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 
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
chartl 97e1a5262e -ct x no longer includes coverage in the previous bin 
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
ebanks 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... 
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
ebanks 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. 
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
ebanks c59c8b9872 Phase I of my promise to Mark: fleshed out integration tests for Indel Realigner 
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
carneiro 75bd0129e7 quick bug fix. 
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
ebanks 9357bee921 Don't skip tri-allelic alleles passed in - just choose the first one. 
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
carneiro a2301383bb quick walker to find out where the reads mapped to huref were mapped in the consensus reference. 
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
ebanks 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... 
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
ebanks d7f98ccd9c Adding --doNotWriteOriginalQuals argument to BQ recalibrator 
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
depristo 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. 
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
depristo aa4a4e515d Safer interface for ReorderSam. Better error checking. Documentation. Moving into Picard now 
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
depristo cd7a7091ba Lexicographic error points users to the ReorderSam wiki entry 
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
depristo 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 
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
kshakir 290afae047 GSA-423 Better reporting for errors in QScript.script(). 
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
kiran 52f860c9b2 Modified MD5s to account for Andrey's new MNP column in CountVariants. 
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
kiran cb95e68fc0 CpG is no longer a standard stratification. 
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
kiran 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. 
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
delangel 1bc5c7e99b boneheaded mistake, mixed up my min and max 
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
kiran 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. 
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
asivache 7ffcade3c3 Added MNP to recognized and counted event types 
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
depristo 57c66b5602 Supports GQ now 
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
kshakir a189454343 FCP only adds the expand intervals QFunction once per script instead of once per QFunction using the ExpandTargets scala trait. 
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
delangel f1d708f4d4 Fixes for HRun annotation in case of indels: 
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
asivache 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 
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
asivache 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): 
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
fromer 6e291820d3 GeneNamesIntervalWalker outputs all genes in each interval; walkers now require a ROD named "intervals" 
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
fromer b304ced801 Updated haplotype calculator to correctly terminate haploptypes RIGHT BEFORE an unphased het 
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
depristo 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 
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
kshakir d185c2961f Added pipeline for calling FCP in batches called MultiFullCallingPipeline. 
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
fromer d6e3f2eba6 Added GC content calculator for CNV data 
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
asivache 7a11b4f35d Another change in variant classification values 
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
asivache 7f7d7eb2d1 Inconsequential changes, more 'variant classification' values are recognized 
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
kiran 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. 
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
hanna 8d6db5d188 Additional logging of the temp file creation, management, and merging process 
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
asivache 03482bf7c4 Number of MQ0 reads in each sample (format field) 
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
asivache 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. 
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
ebanks 9554df1a7c Adding integration test for indels in VF 
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
hanna b992abb6eb A few more unit tests plus some extra 
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
kshakir 4d1cca95bb Removed deprecated getDbsnpFile. 
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