afeb0f63c3
Further, smarter modifications to R script for correctly accessing database data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5124 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-29 03:32:20 +00:00
4f2882c546
Fixing the way that lanes are pulled into from the database so that multiplexed lanes are handled and older sequence data ids are properly handled.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5123 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-29 02:40:10 +00:00
4ee4fd47e9
Moved the test name and the job queue into the spec.
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Defaulting to the hour queue for running pipeline tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5122 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-29 00:07:25 +00:00
2ef66af903
Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high.
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Moved the BamListWriter from FCP to ListWriterFunction in the Queue core.
Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s.
Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 23:33:58 +00:00
04d66a7d0d
Updated integration test's MD5s reflect the fact that assay sequences were previously designed incorrectly for indels, the bug is now fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5120 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 23:00:22 +00:00
5934b9cb82
Augment function isChrM by allowing "CRS" in addition to "chrM" or "MT", as a standard contig name indicating the mitochondrial chromosome. CRS stands for Cambridge Reference Sequence and is the standard in the field.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5119 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 22:45:45 +00:00
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
a2e2a6a9c3
A script to convert an intervals file into a sorted unoverlapping intervals file. Super fast implementation using multiple hashes, should do the job instantly no matter how big the intervals are.
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ps: this utility is similar to -im on GATK, but for queue scripts we need the intervals file fixed before we can run Unified Genotyper because of scatter-gather.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5117 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 21:46:41 +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
b25d131481
updated to work with the new tearsheet
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5113 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 18:49:11 +00:00
bccc71c481
updated to work with the new tearsheet
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5112 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 18:46:38 +00:00
1d8412d652
Updating a few graphical parameters and making sure everything fits together
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5111 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 18:44:23 +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
88ea60b864
Updates formatting and combines plots into the tearsheet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5109 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 17:45:23 +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
cae4b9b0de
quick update with the correct CEU trio bam file and it's final location.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5098 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 19:17:19 +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
68729045ca
Always best to use the left-aligned version of the dbsnp vcf
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5091 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 20:21:50 +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
73e2942c62
Reformated backdrop--removed the date
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5086 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 18:25:59 +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
df2e7bd355
Disabled FCPTest whilst we figure out where the C426 bams went.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5078 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 05:11:57 +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
ce5b11317b
Moved some shutdown logic from the LSF job runner into the QGraph.
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Because of Java's type erasure JobManagers must provide runtime access to the runner class to shutdown.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5076 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 20:28:54 +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
corin
kshakir
asivache
scalvo
carneiro
fromer
depristo
kiran
hanna
ebanks