a0231f073f
Damnit. Enabling the Picard code to recalculate all of the relevant SAMRecord attribute tags means that I need to have reference bases over all read bases even after realignment (and there are some big indels in dbsnp). Fortunately, I have my trusty IndexedFastaSequenceFile reader handy! Re-enabling the previously broken performance test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4255 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 05:06:37 +00:00
7b113a4886
Truncate the floating point numbers coming out of the variant recalibration walkers. Integration tests now work with both 1.6.0_16-b01 and 1.6.0_21-b06
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4253 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 18:37:49 +00:00
cf33614ddc
remove the test that's failing the performance tests, please don't release until this is figured out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4251 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 06:30:40 +00:00
4adb07683d
all fixed..thanks Matt!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4250 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 06:18:59 +00:00
bd4bc84abd
comment out the broken aligner test again - I'll take a crack at fixing it tomorrow. Each software engineer is going to take a pass at fixing it, and we'll see who can do it with the most style.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4249 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 05:22:24 +00:00
61e848c4f0
It's clear from Sendu's calling and my own calling that -qScale 100.0 is a much better default value for low pass data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4248 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 01:47:21 +00:00
e183b6598c
- Fix our private repository of bwa reference support files.
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- Update the test to point to our repository.
- Update the md5 to reflect new Picard tag ordering.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4247 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 00:29:26 +00:00
4183e8805a
Fixed reference (via busted symlink) /broad/1KG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4245 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 20:34:51 +00:00
aeb897db7f
VR walkers look at by-hapmap validation status by default. Eric will be updating the syntax to allow for more flexibility here.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4242 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 15:40:56 +00:00
d7f55574e2
Re-enabling aligner integration test now that we're back to having more than 1 or 2GB memory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4241 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 15:09:48 +00:00
d625186796
I think the VR integration tests are fine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4240 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 15:00:41 +00:00
6a30617a60
Initial implementation of UserError exceptions and error message overhaul. UserErrors and their subclasses UserError.MalFormedBam for example should be used when the GATK detects errors on part of the user. The output for errors is now much clearer and hopefully will reduce GS posts. Please start using UserError and its subclasses in your code. I've replace some, but not all, of the StingExceptions in the GATK with UserError where appropriate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4239 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 11:32:20 +00:00
65edbced36
Addition for Tim: recalculate the NM and UQ tags after realignment. Also, don't fix the insert size calculation, since that's done by fix mate information.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4227 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-08 04:02:14 +00:00
e3962c0d13
VR integration tests are longer but much more useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4210 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 15:50:19 +00:00
b59d62927e
Fix busted performance test (-outputBam has been deprecated in the BQ recalibrator in favor of -o)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4201 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 12:51:53 +00:00
70bb480939
The battle is over. Picard is revved.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4200 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 05:28:01 +00:00
0bb05fb472
Bug fix in VariantRecalibrator. Only add sample names from the input rod bindings, not from all rod bindings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4194 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-02 21:12:09 +00:00
dc5f858d29
Replaced placeholder support for splitting by read group with read support (sorry everyone), and added relatively comprehensive unit tests to ensure that splitting by read group works.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4190 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 22:24:50 +00:00
b28f63a948
Base recalibrator now uses -o and deprecates -outputBam
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4189 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 22:13:50 +00:00
33400074fa
Updated tribble BED parsing code to use the official UCSC spec, and updated tests to match expected results.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4188 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 21:49:06 +00:00
469bbaa240
Added more integration tests for the variant quality score recalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4181 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 15:31:24 +00:00
8c4009ee18
Oops, don't enable reporting in integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4179 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 22:56:18 +00:00
3d6c4fc55f
Removing the obsolete --hapmap and --hapmap_chip options
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4172 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 16:57:05 +00:00
b33873206a
GATKRunReport now has an ID (random 32 char string) that uniquely identifies the JOB run and can be used to find a run in the run repository
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4171 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 16:18:57 +00:00
3fd2392090
Improved interface to getting command line options. Now fully traverses all objects to get all internal argument collections. Preliminary (but disabled version) of phoning home (see -et argument for more information). Captures correct and erroring out runs and writes out gzipped, xml report with lots of useful information. Needs a bit more information but is approximately working. Reports going to /humgen/gsa-hpprojects/GATK/reports/ in submitted directory that will be collated by some external tool. Only operating if -et STANDARD or -et STDOUT are provided currently and REPORT_DIR contains a file called ENABLE. WalkerTest now adds -et NO_ET to tests to avoid populating the reports with tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4155 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-28 22:53:32 +00:00
9c3f403307
Add the calculated lod value to the info field of each recalibrated VCF record.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4153 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 21:33:58 +00:00
bfcac33e80
Cleaning up playground utils and tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4136 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 01:25:47 +00:00
d773b3264b
Eliminated -mrl option.
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Eliminated -fmq0 option.
Eliminated read group hallucination.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4133 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-26 21:38:03 +00:00
dfae48cee0
Moving supported tools to core
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4127 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-26 13:56:19 +00:00
45d895dcf4
Remove the check in the Unified Genotyper for hitting the max reads at locus value. Instead, simply add a flag to the INFO field if any of the samples has been downsampled. 95% hooked up.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4126 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-26 05:50:47 +00:00
79cd716671
More cleanup of the Genomic Annotator. Also, we now require join tables to have unique entries for the column keyed on the join.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4124 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-26 04:43:52 +00:00
dd7f136298
Office-mate courtesy: fixing Andrey's busted integration test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4123 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-26 02:00:06 +00:00
4678613893
Significant fixes for the Genomic Annotator.
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1. Rip out all of Ben's code intended to circumvent the stable VCF Writer output system in multi-threaded mode (I threw up a little when
I saw this code). This will improve memory consumption when running with -nt.
2. Don't annotate indels or > bi-allelic sites.
3. Fix bug where not all records were making it into the output VCF.
4. General code clean up.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4118 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 20:16:50 +00:00
5623e01602
GenerateVariantClusters and VariantRecalibrator now uses hapmap and 1kg ROD bindings (in addition to dbsnp) to distinguish between knowns and novels. It no longer looks at by-hapmap validation status so providing hapmap is highly recommended. Example on the wiki. Input variants tracks now must start with input.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4113 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 18:33:40 +00:00
bf0b6bd486
Update integration tests to use the new ROD syntax.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4112 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 18:13:30 +00:00
3dc78855fd
Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax
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(-B:name,type file) as well as the old syntax. Also, a bonus feature: BAMs can now be tagged at the
command-line, which should allow us to get rid of some of the hackier calls in GenomeAnalysisEngine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4105 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 03:47:57 +00:00
85007ffa87
Some clean up for the variant recalibrator. Now uses @Input and @Output so that it can join the Queue party. Users now specify a -o, -clusterFile, -tranchesFile, and -reportDatFile. Example on the wiki. ApplyVariantCuts now has an integration test. Base quality recalibrator now requires a dbsnp rod or vcf file. Now that the base quality recalibrator is using @Output the PrintStream shouldn't be closed in OnTraversalDone.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4101 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-24 20:14:58 +00:00
90aef66ec5
Minor fixes for my last commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4090 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 23:25:29 +00:00
ccda4f6ec1
More output consistency changes (updating wiki docs as I go along).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4086 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 18:46:08 +00:00
c9c6ff49c2
Deprecated 'O' in favor of 'o' in the cleaner
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4085 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 18:09:24 +00:00
2d3b6d89dc
adding the ability in Tribble to create indexes from a stream of features, so that we can create multiple indexes from one pass of the file. In the GATK we now create multiple indexes, and choose the
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most appropriate based on feature density, and the longest feature in the file. Also:
- Converted Tribble to TestNG; it has better features and is about 6x faster.
- As much code clean-up as I could get done. More to do, especially in the example code.
- Moved asserts in the code to throw exceptions.
- Added getBinSize to the index interface; both indexes already implemented this.
- Removed the abstract parts of the indexCreator interface; this is now more simple.
- Added an IndexType enumeration; might be overkill but it is at least a single point of entry for index information.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4082 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 06:54:59 +00:00
8252494fa9
Forgot to update UG performance test to reflect the new -o argument.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4079 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 00:57:16 +00:00
c177801d81
Add deprecated command-line arguments, and switched over UG to output to
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-o/--out instead of -varout. Let's watch as our intrepid support engineer
gracefully responds to all the incoming questions of the form: "the GATK told
me to use -o instead of -varout. What do I do?"
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4078 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-22 21:01:44 +00:00
b80cf7d1d9
Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4077 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-22 14:27:05 +00:00
121b4f23b6
Simple change to allow a list of samples or regular expressions to be provided in a text file (one line per sample).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4074 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-21 00:01:48 +00:00
fa36731faf
fixes for VariantEval integration tests affected by the spaces to underscores change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4070 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 22:43:20 +00:00
1ec305cd15
Fix for running the cleaner at the lane-level for known indels only: instead of relying on the reads to get the reference sequence, we now use an IndexedFastaSequenceFile in all cases and pad the reference with bases on either end. This allows us to deal with cases in which we are trying to clean just a single deletion-containing read with tiny LOD (so the read needs to be pushed off the seen reference; @Reference doesn't yet work for Read Walkers) and has the added benefit of allowing us now to get much larger known indels that aren't completely covered with reads.
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Thanks to Matt for the advice.
Also, for Guillermo: while I was at it, I changed the .stats debug output to emit the original interval instead of the cleaned region.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4058 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 11:31:13 +00:00
8f15b2ba72
Memory optimization for the VariantRecalibrator. Only add variants to the list if they pass the novelty and qual filters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4051 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-17 21:57:28 +00:00
e632d9b83d
remove some dependencies on out of date methods from the tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4047 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-17 00:07:26 +00:00
c1df293feb
remove testing code from tribble track builder, set the command line program in walker test to null to reclaim memory in integration tests, and removed some orphaned intergration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4046 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-16 23:52:01 +00:00
ebanks
rpoplin
aaron
hanna
kshakir
depristo
kiran