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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
8d389e149f
Now can deal with input files that contain multiple copies of the same event. Only one assay sequence will be designed for each distinct variant, redundant variants will be discarded. Redundancy is defined as same start, same variant type, same ref and alt alleles (it does not matter, e.g., what the sample was as we do not record sample information anywhere).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5115 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 21:42:29 +00:00
9cb1ae384c
Constant precision for floating point numbers. Added integration test - carries over tests from VariantEval with the necessary modifications to command-line arguments and md5s. Disabled use of 'synchronized' keyword because I clearly don't get how that keyword is supposed to work yet...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5107 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 05:19:18 +00:00
f29bb0639b
Documentation and cleanup of the distributed GATK implementation. Detailed documentation -- given that Matt will be extending the system in the near future -- about how the locking and processing trackers work. Added error trapping to note that distributed, shared-memory parallelism isn't yet implemented, instead of just not working silently. General utility function for the analysis of distributedGATK operation in the analysis directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5106 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 03:40:09 +00:00
f036a178f1
Added support for MAF features. So far works for MAF Lite only, annotated MAF is NOT TESTED yet AT ALL.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5105 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 03:20:46 +00:00
ac3fd567b4
Ugly one-off error fixed in building design sequences for indels: the event position is immediately *before* the event, so the ref base at the current locus is the base immediately *before* [ref/alt] element
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5103 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 02:53:03 +00:00
3e9f185dad
Fixed issue with GenotypeConcordance being initialized incorrectly when the first seen comptrack had no samples.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5102 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 01:12:27 +00:00
58f0ecff89
Fixes to support evaluations with TableType elements - each such object now gets a separate entry in the output table. Added codon degeneracy stratification. Handle null elements in reports (useful for debugging).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5101 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 22:09:59 +00:00
a264b16358
Patch from Brett (with minor tweaking by me) to expose all the relationships
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of a particular sample in hash format. Thanks, Brett!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5100 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 21:46:13 +00:00
61c29d550d
Fix for NullPointer where a run starts but there's nothing to do (no shards) and reduceInit() wasn't being called correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5096 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 15:15:10 +00:00
d33162145b
Moving the --sites_only argument up into the VCFWriter itself so that any walkers that write VCFs can choose not to emit genotypes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5088 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 19:38:16 +00:00
22e599ec76
Fixed output report to properly handle evaluation modules with TableType objects. Promoted CpG to a standard stratification. Demoted Filter to a non-standard stratification. Now, if the filter stratification is not specified, VariantEval only evaluates PASSing sites.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5084 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 17:38:21 +00:00
0429301536
Added ability to output just sites (no genotypes) from UG with the --sites_only argument. Note that we do still genotype in this mode so that the INFO annotations are identical, but we strip the genotypes out of the VC right before writing to output. In other words, this is not designed to make UG go faster; the point here is to allow downstream tools not to have to parse GTs if they don't want to. Here you go, Ryan.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5081 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 14:52:38 +00:00
01e032e89c
Missorted BAMs are User Exceptions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5080 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 14:09:39 +00:00
be697d96f9
An apparently robust implementation of the file locking for distributed computation, using Lucene's file creation locking approach. It is worth trying out for those with large-scale, high-cost data sets. Details and discussion at group meeting on Wednesday. Some cleanup still needed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5079 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 13:45:40 +00:00
db2e2cb0ff
Another trivial change to make VQSR work with indels
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5073 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 19:05:31 +00:00
9db02059ac
Fix for Ryan's issue: reads ending with indel distort the location of the
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pileup, resulting a two map() calls for the same locus (and no map call for
the locus immediately following).
Fixed bug and added comprehensive unit tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5067 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-24 19:49:39 +00:00
c50f39a147
V3 of the distributed GATK. High-efficiency implementation. Support for status tracking for debugging and display. Still not safe for production use due to NFS filelock problem. V4 will use alternative file locking mechanism
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5063 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-24 16:45:07 +00:00
fd864e8e3a
Minimal necessary (but most likely not sufficient) changes to run VQSR on indel data: don't fill Ti/Tv fields if non-SNP, request VC only st start of position, check if isSNP() before doing snp-specific operations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5062 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-24 02:36:36 +00:00
a51061fd96
Improved distributed processing analytics. Still not 100% ready for prime-time. More improvements incoming. Iterator claim now supports requests to obtain in a single atomic claim (one lock) multiple sequential shards, which radically reduces overhead. However, deadlocking is still possible...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5061 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 16:17:25 +00:00
2d4bcb60a1
Don't print out alt alleles for ref calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5060 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 06:33:31 +00:00
2ba35dc7ba
Bad chain files are user errors
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5059 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 06:04:36 +00:00
2bbcc9275a
Committing the fragment-based calling code. Results look great in all datasets (will show this at 1000G this week with Ryan). Note that this is an intermediate commit. The code needs to be cleaned up and the fragmentation code needs to be moved up into LocusIteratorByState. This should all happen later this week, but I don't want Ryan to have to keep running from my own personal Sting directory. The current crappy implementation adds ~10% to the runtime, but that should all go away in the next iteration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5058 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 05:04:17 +00:00
9b1b8d46aa
Performance tracking of GenomeLocProcessingTrackers, as well as a marker for where to put tracker in HierarchicalMicroScheduler
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5051 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 22:24:42 +00:00
95d6ddc38c
lastProgressPrintTime should only be updated when a progress log is printed not when a performance log is printed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5050 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 22:23:14 +00:00
78a43faebe
Adding options to warn instead of erroring out (so that you can see all errors in one shot) and to skip filtered records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5042 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 05:24:28 +00:00
02b5d4357f
Deprecated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5041 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 05:05:07 +00:00
c3dbbe7f91
Bug fix: don't assume users won't use arbitrary rods on the commandline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5040 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 04:59:28 +00:00
hanna
ebanks
delangel
depristo
asivache
rpoplin
chartl
carneiro
kiran
fromer
scalvo