6ebca5d219
Enhancements to build external projects for walker sharing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4348 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 21:17:16 +00:00
eb1fa4bff3
changes an argument to an output so I can use it to track dependencies in queue
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4347 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 21:07:09 +00:00
9cf079e1bb
Ready for integration with queue script
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4346 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 19:46:01 +00:00
3ec0e09edd
ADPR is now included in the full calling pipeline. The most up to date version of the ADPR is about to be committed and should be used with the script for now. The qscript now calls for two additional strings as inputs: the sequencing machines used and the sequencing protocol. In order for ADPR to finish successfully, a squid file for both the lane and sample level data needs to be produced, reformatted and named <projectBase>_lanes.txt or <projectBase>_samps.txt, respectively. These files need to be in the working directory. When database access is ready, this and the protocol and sequencer parameters of the r script will go away.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4345 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 19:28:43 +00:00
0cc48d46ec
Escaping quotes in dot files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4344 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 17:13:12 +00:00
745b8cc6d3
GATK now detects and UserExceptions when human lexicographically sorted data is provided
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4343 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 15:19:48 +00:00
67bcf3a7e4
Fixed VariantEval rod binding names.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4342 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 14:52:51 +00:00
1931b2e1bd
Three fixes for VariantFiltrationWalker: Trying to filter an empty VCF file will produce a well-formed VCF file with zero records instead of a blank file, needed for pipelines. The first record's genotype info fields are now in the same order as all the others. The VCF header lines are pulled from just the input variant rod instead of from all rods.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4341 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 13:52:56 +00:00
c355afc320
Queue now does job tracking (replace -run with -status in the command line). Produces output that looks like:
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INFO 20:58:17,827 QCommandLine - Checking pipeline status
INFO 20:58:23,234 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_MergeIndels [DONE]
INFO 20:58:23,236 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_158.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,237 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_929.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,238 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_SNP_calls [NOT DONE] 5t/0d/0r/5p/0f
INFO 20:58:23,239 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_HandFilter [NOT DONE]
INFO 20:58:23,240 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_1122.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,240 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_VariantRecalibrator [NOT DONE]
INFO 20:58:23,241 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_913.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,242 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_2037.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,243 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_VariantEval [NOT DONE]
INFO 20:58:23,244 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_Cluster [NOT DONE]
INFO 20:58:23,245 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_106.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,246 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_Cluster_and_Indel_filter [NOT DONE]
INFO 20:58:23,247 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_ApplyVariantCuts [NOT DONE]
INFO 20:58:23,248 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_GenomicAnnotator [NOT DONE]
INFO 20:58:23,248 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_1713.bam [DONE] 5t/5d/0r/0p/0f
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4340 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 00:59:09 +00:00
4ed9f437e9
Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts.
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The GAE half has all the walker specific code. The new "Abstract" GAE has the rest of the logic.
More refactoring to come, with the end goal of having a tool that other java analysis programs (Queue, etc.) can use to read in genomic data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4339 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-23 23:28:55 +00:00
0c9fabb06f
Fix in AnalyzeAnnotations, somebody changed it look for ID in the vc's info field. This dinosaur desperately needs integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4338 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-23 19:48:44 +00:00
0c781968fb
Tried to do a bit of pre-commit refactoring and screwed it up. Fixed.
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Thanks to Ryan for identifying the problem.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4336 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-23 18:17:29 +00:00
d6bd1debeb
This is an updated version of the automated data processing report. Each page in the report is a stand alone function, which are linked together with a function which pulls all appropriate data (assuming a standard naming convention) and generates the pdf. This script still need to respond appropriately when it doesn't find the data it needs, database access, and a way of getting some information from sequencing for the tearsheet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4335 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-23 18:08:16 +00:00
d081b9b352
Improvements to error messages about @Requires and @Allows
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4334 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-23 12:08:27 +00:00
7841b301c4
Added more diagnostics so that I have some idea of what a 'general' exception
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is. Required to fix bug ZjhCJAdwhtFq1x54ZlmlN8pFNcbrRpdJ and similar. We
might want to change this particular case to a ReviewedStingException after
we gain a bit more experience with it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4333 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 21:32:01 +00:00
44ccfc3531
Updated Phasing algorithm + evaluation module to properly implement haplotypes [including homozygous genotypes]; Implemented dynamic window phasing model for LARGE increase in efficiency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4332 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 21:29:58 +00:00
192757d1e0
Added the new pipeline classes to the StingUtils.jar so that ant test picks them up.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4331 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 20:05:22 +00:00
8f75d88519
Fix for GATK run report ids:
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mOVsxGfDiiSMxVs2PPTVjzYTVbizlD6e
f9kUHUADFsZ0LiTGxRL5zPmq9kZcA4cQ
8eGHWJFAlBVmgxwPi3sMd1RmiN2PwHOf
iLhvHWveypKb2F8vKS5irHylc3pYvlOb
HDttXKUMEVoPrvVeWrH7E0htxYyNydMx
plus a bit of cleanup of custom exceptions in the sharding system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4330 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 19:49:25 +00:00
20b38b38f3
Updated from SnakeYAML 1.6 to 1.7.
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Added a pipeline java bean and YAML utility to serialize java beans.
Added a getFirehosePipelineYaml.sh that can pull firehose data into the pipeline yaml file format.
Updated the fullCallingPipeline.q to begin using the pipeline yaml file format for bams and reference.
More changes to come as this code gets tested out in the fullCallingPipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4329 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 19:47:49 +00:00
d9b8fa2acc
Up the memory required for integrationtests until we can figure out why
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memory isn't being freed correctly when multiple integration tests run as
part of a single class.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4328 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 18:54:24 +00:00
fb5d595ef0
Disable VCF header output in the Beagle integrationtest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4327 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 16:50:03 +00:00
0c99c97685
The engine now automatically adds the command-line arguments to the header of every VCF, unless -NO_HEADER is specified.
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Changed integration tests, adding the -NO_HEADER argument, for walkers that previously did not include the command-line
arg headers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4326 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 15:27:58 +00:00
1af9ca6d45
enabling tests that now pass with the conitg length validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4325 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 22:20:50 +00:00
6dec042288
Re-enabling indel cleaning, explicitly calling fix mates in the case where indel cleaning is not scatter/gathered
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4324 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 20:37:49 +00:00
522830fb01
Support for --assume-single-sample in UG, better malformated bam exceptions, and ignoring out of order contigs in seqdictutils. All for the CG bam file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4323 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 20:33:34 +00:00
3938d53738
one broken build short of the hat trick. Fixing the unix test which expects the sequence dictionary of the Tribble track to equal the reference; we actually return the sequence dictionary of the track iself, with each contig set to the length of the sequence dictionary contig entry.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4322 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 18:47:20 +00:00
b968af5db5
The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4321 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 18:21:22 +00:00
2586f0a1ca
fix for the build I broke - the original file got corrupted, which I replaced with a version that didn't have the header stripped off. Other integration tests passed, but this test relied on the header being stripped off.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4320 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 15:35:25 +00:00
547763b230
Better error message for Petr's null pointer exception. Also added an exception integration test because I'm certain this used to work.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4319 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 13:44:40 +00:00
8719dde59d
Now prints out PASS when a variant is unfiltered
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4318 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 13:16:41 +00:00
21a34daf2e
add playground classes to the jar (if they are compiled). Thanks, Khalid!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4317 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-20 22:28:08 +00:00
f9707bb7bf
Fix for Matt: For Mac OS 10.6 temporary directories replace paths like '/var/folders/Ax/AxRUoz51Fh05fVe-j6C1Wk+++TI/-Tmp-/' with '/tmp/' so that google reflections 0.95RC2 still works on classes in the directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4316 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-20 22:02:07 +00:00
205fc0b636
Cleanup: Use Tribble's version of createVariantContextWithPaddedAlleles (no real functional difference) to avoid duplicated code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4315 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-20 19:53:30 +00:00
a10cfe213b
Small bug fix in simple indel genotyper: Likelihood of case where best haplotype pair was (REF,REF) was not computed correctly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4314 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-20 17:04:39 +00:00
f5a30d0248
I just spoke to Andrey & Kiran (the original authors of these tools), and they voted to kill these in favor of Picard
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4313 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-20 13:27:35 +00:00
b24172c80f
Queue now utilizes .[file].done to allow skipping of previous jobs, if they have been completed. This is, unfortunately, reliant on a python script to do the post-execution touching of .done files.
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That is to say, proper resumability is live (but not extensively tested)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4312 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-20 00:16:53 +00:00
f64b6fddc1
Major changes/improvements to indel genotyper:
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a) Redid way to compute path metrics in indel error model. Paper formulation where we have an anchor point in the alignemt between read and haplotype won't work in practice except in nice data sets that are perfectly indel-realigned and that are well mapped by aligner. New formulation doesn't assume this, and it's actually simpler and uses less code. It now resembles more a classic SW dynamic programming formulation but it still preserves the HMM probabilistic formulation.
b) Added a programmable call threshold, set by command line.
c) Use now sample name from BAM file, remove -sampleName argument.
d) Simplify loop to compute read-haplotype likelihoods.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4311 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-19 23:47:31 +00:00
40274ba7dc
Do this the right way
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4310 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-19 04:30:48 +00:00
fa8cfd3031
Adding this to get around lsf/csh issues (see recent help message). Also seems like a good time to reiterate http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4309 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-19 02:45:16 +00:00
c6351a11d6
Clearer logger output when not using by-hapmap
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4308 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-18 16:10:42 +00:00
7e58d8ed61
CombineVariants now outputs the command line in the VCF header. Added a new hidden argument to VR walkers called --NoByHapMapValidationStatus to turn off the by-hapmap dbsnp rod behavior. Very useful for experimenting with which sets to use as training data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4307 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-18 16:06:50 +00:00
6f6d2eb31f
Told people this worked...forgot to commit!
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-c
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4306 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-18 03:46:00 +00:00
a3f31e5df0
When QScript writers use the RodBind, then the File version of the same argument should be optional, i.e. should not always try to output the file, which when unpopulated will be null.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4305 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 18:22:07 +00:00
1c94a73434
Fixed header generation when lines contain spaces.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4304 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 17:14:59 +00:00
c6c6d32b46
Quickly adding a new convenience method for retreiving a group of samples. The method is getSamples(Collection<String>) and returns a set of sample objects. There's also a test there.
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Ryan is using this to modify VCF code today...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4303 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 15:55:17 +00:00
a898908918
The output BAM file optional arguments of compression and whether to write an index are not outputs themselves.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4302 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 15:35:54 +00:00
bc12055fcf
Quick patch to fix the sample code. It wasn't actually initializing the sample data source, so I added a call to initializeSampleDataSource() in GenomeAnalysisEngine. I think there was just an error resolving the versions of GenomeAnalysisEngine
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Also added a new error message that I thought would be helpful...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4301 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 14:05:26 +00:00
a10b2a00a5
Moving the util VariantContext 'modifying' routines into VC itself (as opposed to VCUtils) so that we can pass the genotype data directly into it and are no longer forced to decode the genotypes for no reason. This means that any walker that takes in a VCF and modifies the records without touching the genotypes never have to decode them. I've hooked this into the other two Variant Recalibrator walkers for Ryan. One side effect, though, is that we no longer can sort the sample names in the VCF (i.e. if the input VCF doesn't have samples in alphabetical order, then we used to sort them when writing a new VCF but no longer do that), because if we don't decode then we can't re-order the genotypes. I don't think this is a big concern given that the Unified Genotyper does emit sorted samples and that's the main source for most of the VCFs we use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4300 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 07:09:58 +00:00
f66ef4626e
Fixing two minor issues: 1) adding a new error message if the user adds a fasta file in a directory that doesn't exist; 2) renaming my sample unit tests so they actually run.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4299 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-16 20:45:51 +00:00
3a400e3dc0
Added CountCovariates integration test to ensure that it throws an exception if a variant mask isn't provided.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4298 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-16 19:18:38 +00:00
hanna
corin
kshakir
depristo
rpoplin
chartl
fromer
aaron
asivache
delangel
ebanks
bthomas