2ef66af903
Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high.
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Moved the BamListWriter from FCP to ListWriterFunction in the Queue core.
Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s.
Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 23:33:58 +00:00
04d66a7d0d
Updated integration test's MD5s reflect the fact that assay sequences were previously designed incorrectly for indels, the bug is now fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5120 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 23:00:22 +00:00
5934b9cb82
Augment function isChrM by allowing "CRS" in addition to "chrM" or "MT", as a standard contig name indicating the mitochondrial chromosome. CRS stands for Cambridge Reference Sequence and is the standard in the field.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5119 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 22:45:45 +00:00
7af0532292
An attempt to have more intelligent sorting of RODs. Tested with maf only so far. Should be able to reference-sort dbsnp, bed and vcf as well, bugs nonwithstanding. Very simple, brute-force implementation using SortingCollection. Should I have used tribble indexing machinery instead?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5118 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 22:10:07 +00:00
fa8963522b
Ignore header line if it happens to be passed to the codec again, instead of crashing on it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5116 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 21:44:33 +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
f2de39d661
Calculates phase concordance rates between trio and RBP-phasing tracks, stratified by trio status (Het3, non-Het3)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5114 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 20:50:01 +00:00
ffd5f407a5
Retain only a single walker to perform calculation of haplotype extents
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5110 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 18:33:32 +00:00
2182b8c7e2
Better query start / stop function that directly parses the cigar string, unlike the previous version. Now properly handles H (hard-clipped) reads. Added -baq OFF and -baq RECALCULATE integration tests on all three 1KG technologies. Please let me know if this new code somehow fails.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5108 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 15:08:21 +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
91e4bb0285
Added walker to calculate haplotype lengths for ALL fragments produced by stitching together phased sites (actually, stitching together everything BUT unphased het sites)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5104 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 03:09:20 +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
9c728979cc
In order to calculate haplotype lengths of trio+RBP, I implemented a simple trio phaser as an option to ComparePhasingToTrioPhasingNoRecombination, which already decides if the trio could theoretically phase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5099 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 20:17:48 +00:00
5ed128f839
Slightly more tolerant timing setting. Main() method in GenomeLocProcessTracker to generating timing data for trackers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5097 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 15:16:07 +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
f522eb2848
Previous tests were just too big...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5095 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 13:48:38 +00:00
2901299ff6
Sets the number of samples to all of the samples in the file when it's not specifed on the command-line explicitly. GenotypeConcordance no longer a standard evaluation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5094 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 01:38:26 +00:00
4a33cdacde
Some basic integration tests detecting breakage in OTF BAM index generation.
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Doing it manually for the moment so that there's at least something testing
this capability; will followup eventually with Mark to see whether we can
shape the VCF index generation code in such a way that it supports BAM index
testing as well.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5093 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 23:48:04 +00:00
466f8f8a3c
Compares RBP phasing to a simple trio phasing model that can phase a child het iff both parental genotypes are known and at least one of them is not het [at EACH of the sites in the pair to be phased]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5092 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 23:43:29 +00:00
43812a28fc
If among all the multiple alignments for the given read we have 'unmapped' ones (can happen with bwa 0.5.7 and maybe later versions), then discard the latters and keep only the mapped ones. Keep 'unmapped' only if its the only alignment available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5090 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 20:07:08 +00:00
63b709d992
When remapping the read, set MAPQ, CIGAR etc to 0/null for unmapped reads. This is not required according to spec but current samtools jdk otherwise dies in STRICT validation mode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5089 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 19:49:07 +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
a97184fddf
Frick! Changed to refer to the *playground* version of VariantEvaluator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5087 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 19:33:03 +00:00
a9d0772516
When evaluating JEXL expressions, on't blow up if the eval VC is null
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5085 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 18:25:03 +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
2dcce58279
oneoffs walker to assess GLs at truth sites
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5083 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 14:59:05 +00:00
dfc5a3d1f3
added integration test for --sites_only option
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5082 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 14:58:15 +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
862b299b47
Fix Picard OTF index generation issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5077 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 03:42:46 +00:00
6ac888d26a
Correct accounting for cases where first het in interval is phased
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5075 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 19:48:54 +00:00
af79fa629f
PROPERLY print out list of intervals and their stats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5074 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 19:20:36 +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
17ba75e502
Can now print out list of intervals and their stats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5071 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 18:36:59 +00:00
9923e05e0a
Moved MD5 utils from WalkerTest to BaseTest for use by PipelineTests.
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Moved VariantEval validation from FCPTest to PipelineTest.
Cleaned up some duplicate code for writing temp files during tests.
Moved FCPTest to playground namespace to match move for FCP.q.
Added a basic HelloWorldPipelineTest for the HelloWorld QScript.
Moved duplicated error handling from JobRunners into the FunctionEdge.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5068 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 04:11:49 +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
61fe409211
Basic walker to count the number of (phased) hets in each exome target
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5064 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-24 17:53:14 +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
bb6999b032
Better documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5057 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 03:36:09 +00:00
kshakir
asivache
scalvo
fromer
depristo
kiran
hanna
ebanks
delangel