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
4979dcc9a7
Finishing up the playground cleanup (for now)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4135 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 01:19:37 +00:00
0452b1ab68
archiving, removing, or promoting to core from playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4134 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 01:07:42 +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
f384d4a5d6
A java reimplementation of vcf2table in python; supports getting more useful information about genotypes (HET, e.g.) than was possible in python.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4130 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-26 17:50:33 +00:00
1e193e4c20
prinring '\n' at the end of line leads to some aesthetical advantages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4129 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-26 16:29:42 +00:00
9b3ffa5f64
Now outputs VCF (as standard output associated with -o)! Can also outptut, in parallel, a lightweight bed and fully annotated .txt (old verbose format) with --bed and --verbose, respectively
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4128 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-26 16:26:03 +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
e06b2c90ef
Cap the default size of join tables; this can be modified with the --maxJoinTableSize argument. Also, misc cleanup of the comments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4125 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-26 05:21:26 +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
0105e8d063
Updated Queue GATK generation to reflect -B and -I changes.
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To add support for "-I:tumor tumor.bam", the GATK argument
import_file (-I) is now generated as a List of NamedFile objects.
Could not get sugar working 100%. To activate sugar import the
gatk package. This effectively adds a new method to java.io.File
called toNamedFile. When adding a file to the list call
countReads.import_file :+= myJavaFile.toNamedFile
See scala/qscript/examples for actual examples.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4122 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 22:17:36 +00:00
bdb3a7ebe6
The tagger was automatically combining identical tags, but this is a problem
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for the ROD system. Eliminate tag combine operation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4121 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 22:01:32 +00:00
39da567d48
Changed ReadBackedPhasing to be a RodWalker (corrected to By(READS))
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4120 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 20:53:04 +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
41e53d37e1
Changed ReadBackedPhasing to be a RodWalker (more efficient, since it is ROD-focused)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4117 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 19:43:57 +00:00
ac58eb3cbb
Slightly better error message for the common error of only providing a dbsnp track but giving it zero clustering weight.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4114 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 18:41:21 +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
14198b74d5
Can now compute av. qualities and stddevs per cycle for both original (when present in bam) and recalibrated quals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4111 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 17:14:58 +00:00
23dbaa68e6
Can design assays when multiple (distinct) events occur at the same locus (one assay per event)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4110 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 16:52:47 +00:00
b4baa3eb8f
Cleanup. INDELS model is now disconnected (and renamed 'DINDEL' in preparation for adding plumbing for Guillermo soon)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4106 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 14:52:51 +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
aa8cf25d08
Implemented fully symmetric sliding window read-backed phaser
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4104 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-24 21:12:32 +00:00
cba5f05538
Small fixes for consistency in the numbers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4103 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-24 20:48:25 +00:00
7bbd67f3c4
Fixing stray comments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4102 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-24 20:19:39 +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
f2b138d975
Small refactoring: make Haplotype a public class since it will be soon extended and shared with other callers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4100 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-24 17:52:36 +00:00
43f1fb2380
Okay, finally done with VCF compression. Now:
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1. Uses blocked gzip compression.
2. No more -bzip option available (since we can't compress to sdout).
3. Only file extensions that are compressed are .gz and .gzip.
4. No more need for CompressedVCFWriter.java
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4099 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-24 16:36:54 +00:00
25fb53e7a2
Oops, forgot to call toLowerCase().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4097 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-24 14:43:24 +00:00
7957b60768
We now automatically compress the output VCF if the file suffix is one of the supported types (.gz, .bz, .bz2). You can still specify -bzip if you want to use another file suffix (or pipe it to sdout for some reason).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4096 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-24 14:39:59 +00:00
7a8b6b87da
Committing Michael Yourshaw's patch for AnalyzeCovariates. We spawn each RScript process and wait for it to finish in series. Thanks Michael!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4095 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-24 13:06:25 +00:00
9fb151f417
Minor update
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4094 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-24 05:17:10 +00:00
44f3c5639a
I have finally figured out that when you volunteer to do something in group meeting, you keep getting pestered about it on Mark's Omniplan doc until it gets done (except for contig aliasing, of course). As such...
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We can now emit bzipped VCFs from the GATK.
Details: any walker that defines a VCFWriter for its @Output (i.e. pretty much every core walker from UG and on), also has associated with it the -bzip (--bzip_compression) boolean argument. When set, it will emit a VCF that is compressed with bzip2.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4093 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-24 04:14:50 +00:00
691333f75c
Force isRequired() to be false for @Deprecated args.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4092 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 23:50:30 +00:00
5d6a6420a9
New behavior for filling it output streams: if required==true for a field and the field
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is an output stream, we'll automatically create it and point it to stdout. Otherwise,
we'll leave it empty.
I think about it like this: marking a field 'required' indicates to the GATK that the
walker author requires a value for this field, and if the GATK can provide one without
end user intervention, it will. Maybe this is hackish. We'll try it and see.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4091 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 23:39:13 +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
ef795825fd
Yet more argument consistency updates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4089 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 20:52:30 +00:00
7474afa7a3
allow other objects access to the static method that resolves bam lists, and some renaming and improved documentation for the function.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4087 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 18:52:00 +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
55a8306a0d
Update the @RMD tags to look for VariantContext.class instead of ReferenceOrderedDatum.class. Since the test for rod type is broken this won't affect anything right now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4084 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 17:49:37 +00:00
35b9883dd6
vcfwriter is in tribble now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4083 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 17:01:04 +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
295472bf69
Simple change to handle a no-call (must avoid asking for the second allele, which will be be null in this case). Also, added a hack to deal with input VCFs where there are no genotype likelihoods (needed in order to process Hapmap and 1KG VCFs). In this mode, called genotypes are assigned a likelihood of 0.96, and alternative genotypes are given 0.02 each. I know Beagle actually takes genotype data without likelihoods, so this might not be the right way to do this.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4081 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 05:13:09 +00:00
dec713a184
Simple test code from Steve Schaffner to compute R^2 and D'. This is just for educational purposes. Don't use this code for anything, ever!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4080 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-23 05:06:16 +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
ebanks
hanna
depristo
asivache
kshakir
fromer
rpoplin
delangel
aaron
kiran