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
5b94c926c8
More precise language.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4178 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 21:44:22 +00:00
96040726ac
Better exception text for the common error of providing only dbsnp but giving dbsnp sites zero clustering weight.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4177 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 21:36:43 +00:00
32c6b48106
Proper memory metrics in the file. Please use -et if at all possible
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4175 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 20:30:09 +00:00
63c7cbd89b
Forgot to commit this long ago, change so the tables are correctly propagated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4174 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 19:06:52 +00:00
db4ff7317f
allowing empty RMD files (we need to not validate their sequence dictionaries against the reference in this case)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4173 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 17:45:33 +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
3c956110f3
Fixing up the VCFWriter storage code: instead of assuming all samples are coming from the input bam file (they're not), just use the original VCF header for writing the temporary thread files. Now parallelization in e.g. the Genomic Annotator works.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4168 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 02:16:07 +00:00
69d92fab4f
adding the ability to get iterators from Tribble without having an index, and updating the Tabix code to the latest Samtools SVN version (this still doesn't fix the outstanding tabix bugs, waiting for Heng on that).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4167 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-30 21:49:23 +00:00
50f7f18cbd
Changed ReadBackedPhasing default PQ threshold to 10
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4166 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-30 21:26:15 +00:00
e64d1be475
Check if VC is null before trying to subset it (can happen with indels)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4165 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-30 20:43:37 +00:00
1ddb5d17c9
hostname now fully qualified and working
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4163 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 17:04:37 +00:00
4c28fc3a39
Clear documentation for GATKRunReport
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4161 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 15:59:25 +00:00
16b75e3b9a
A new version of the ErrorRateByReadPosition walker, using the GATKReport functionality to store and emit its output. This version of the walker is roughly half the number of lines as the previous version, owing simply to the removal of all of the output formatting that's now handled by GATKReport.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4160 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 05:41:13 +00:00
fd19c63aaf
A data structure that allows data to be collected over the course of a walker's computation, then have that data written to a PrintStream such that it's human-readable, AWK-able, and R-friendly (given that you load it using the GATKReport loader module).
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This object designed to be both the structure that holds data during the execution of the walker, as well as the object that properly formats and emits the data so that it can be easily loaded into R. In the end, you get a table that looks like this:
##:GATKReport.v0.1 ErrorRatePerCycle : The error rate per sequenced position in the reads
cycle errorrate.61PA8.7 qualavg.61PA8.7
0 0.007451835696110506 25.474613284804366
1 0.002362777171937477 29.844949954504095
2 9.087604507451836E-4 32.87590975254731
3 5.452562704471102E-4 34.498999090081895
4 9.087604507451836E-4 35.14831665150137
5 5.452562704471102E-4 36.07223435225619
6 5.452562704471102E-4 36.1217248908297
7 5.452562704471102E-4 36.1910480349345
8 5.452562704471102E-4 36.00345705967977
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A GATKReport object can hold multiple tables, and the write() method will emit all tables in succession. Each table starts with its own ##:GATKReport.v0.1 table header, so each table can stand alone. This allows for tables to be mixed and matched in a single file, or for the output from different walkers to be combined into a single file with no ill effect.
The display property of individual columns can be turned off. This is useful when a column is used to store intermediate results, necesary for the computation of some later value, but the contents of the intermediate column itself are not required in the final output file.
Finally, the GATKReportTable allows for some simple, mathematical, element-wise and column-wise operations. For instance, two whole columns can be divided, the results of the operation being stored in a third column. This mimics the most basic of R operations, where whole vectors can be added, subtracted, multiplied or divided without requiring the developer to explicitly write a loop.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4159 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 05:39:24 +00:00
df76474b34
Proper filtering when indels are being lifted over
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4158 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 04:48:31 +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
fe19539188
Small bug fix: if a read falls at the edge of an indel event (but is not part of it), don't count it towards consistency computation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4152 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 20:37:27 +00:00
54355b1864
In variant quality score recalibrator Preserve the definition of known and novel to be presence in dbSNP or not even when training with 1KG project calls.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4151 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 19:07:59 +00:00
7a5f297083
actually modify the vcf when a sample has been down-sampled
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4150 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 19:03:21 +00:00
9860db64a3
Fix up liftover to enable lifting over indels
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4148 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 17:55:27 +00:00
fb177c4fee
If only dcov is specified, assume that selected downsample type is BY_SAMPLE.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4147 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 17:35:41 +00:00
9584cbc05e
UG now downsamples to 250x by default
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4146 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 16:53:15 +00:00
431392330e
Re-enable the max records in ram argument, which I accidentally removed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4145 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 16:42:49 +00:00
de5ccfb0b1
Moved hasPileupBeenDownsampled() based on Eric's request. Also eliminated
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@Deprecated constructors from AlignmentContext.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4142 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 16:12:05 +00:00
427a2f85e9
The Indel Realigner now lets the engine do all of the setup for args affecting the SAM writer. Thanks, Matt!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4141 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 15:19:47 +00:00
a3d9d23b0f
Now prints het genotype with GQ=0 for each indel; in two-sample (normal-tumor) mode, prints both genotypes (N and T) as hets for germline events or hom ref for N and het for T for somatic events (all genotypes still have GQ=0)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4140 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 15:06:42 +00:00
dda84a0e54
Re-enabling indels for the Genomic Annotator as per Steve's patch. Steve assures me that he will test this out really well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4139 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 15:01:25 +00:00
6f4af47aac
setMaxRecordsInRam now a member of StingSAMFileWriter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4138 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 14:50:41 +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
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
30a104228a
Don't require entropy reduction when cleaning only at known sites; instead we need to trust the known indels. This will improve consistency between lane-level and aggregated cleaning.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4076 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-22 02:44:38 +00:00
b6989289fc
Potential bug fix for bad references where some codons may have Ns
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4075 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-21 12:09:33 +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
165dc6d3b0
Ryan, what did you decide about supporting this tool? Is it still useful?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4073 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-20 19:16:14 +00:00
2ef2f1b24a
Fix UG's simple indel calculation model so that deletions are created correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4072 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-20 15:35:47 +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
1c4784999a
Updated to work exclusively in log10 space
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4069 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 21:31:07 +00:00
3af4e618cc
Fixed precision issues with PQ (phasing quality)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4068 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 20:34:47 +00:00
88ca1fb22c
Lazy loading reflections so Queue can hack the classpath before the PluginManager looks for classes.
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Removed extra quotes from 'cd' pre-exec command.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4067 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 20:29:52 +00:00
63ada20da5
allow RefSeq files to optionally contain the header line, which is the default output from the UCSC table browser
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4065 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 20:25:37 +00:00
effeedf1a3
Updated Bayesian phasing method to output per-site phasing statistics (and to not cap PQ at 40)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4064 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 19:55:47 +00:00
04e5b28f6d
updates for VCF; we can no longer cache genotypes or alleles in a static array, this is bad for sharred memory parallel runs. One instance per codec was better for performance than using ThreadLocal code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4063 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 19:34:44 +00:00
8054b6b295
Changing a name of a column for variantevals output for easier reading by R--let me know if this needs to be updated elsewhere; it's just a space to an underscore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4062 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 19:18:16 +00:00
4b94f8c21b
Silly me, I forgot to check for the contig boundaries. Thank goodness for performance tests!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4061 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 18:40:26 +00:00
f16bb1e830
fix for a bug in package utils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4060 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 15:01:50 +00:00
15c5aa6e48
Efficient iteration over all possible combinations of variable assignments, for variables of arbitrary cardinalities
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4059 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 14:14:37 +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
98f7679619
Fixed the bug reported on GS regarding a clipped read that got moved several hundred bases away. The code that got triggered here was written back in the original version of the cleaner and it never actually did the right thing.
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While I was fixing it, I noticed that we weren't allowing the cleaner to un-clean reads with indels when they're wrong even though we should. Hypothetically, that should rarely happen: only when we can left-align out an indel or when the original mapper really went haywire. This situation is rare enough that I'm calling logger.info to let the user know it's happening and suggesting that they double-check that everything looks right with their reads. Better to be extra-cautious now that the cleaner is moving into the 1kg and Broad production pipelines soon
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Mark, have no fear: this was truly a rare edge case - one that won't affect the cleaning stats. There is no need to re-clean the data processing paper bams!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4057 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 01:42:48 +00:00
3dc4d3c3a9
removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also
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removed the auto-deletion of the reflections jar, and removed the very old OmniPlan document we had checked-in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4056 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 00:42:37 +00:00
1336ea17a3
quality-scored-based Bayesian phasing algorithm implemented
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4055 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-18 21:17:46 +00:00
553bda4e0e
PreciseNonNegativeDouble permits precise arithmetic operations on NON-NEGATIVE double values
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4054 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-18 21:10:58 +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
b7c60b9729
Queue now uses its own version instead of the gatk version.
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Added a Queue release directory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4050 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-17 19:34:23 +00:00
e632d9b83d
remove some dependencies on out of date methods from the tests
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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
578e7fa36d
Don't output -0 as qual value in VariantRecalibrator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4044 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-16 16:47:58 +00:00
3d63302b70
Deprecated. Use SelectVariants instead.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4043 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-16 15:07:50 +00:00
20db00a3e8
Lazy reference loading; the engine doesn't fetch the reference bases until you actually call ref.getBases(). With the new hidden --dontUpdateUG to table recalibrator this is 2-3x faster than before. Enabled for locus, read, and rod walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4042 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-16 13:46:22 +00:00
9ab647b730
adding checks to the RefSeq rod for line's that contain less than the required number of columns (we expect there to be 16 columns)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4041 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-16 13:34:32 +00:00
cc58a27b00
fix for broken unit test; make sure when we can't get an index off of disk, the internal method returns null
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4040 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-16 13:12:32 +00:00
b23545fafa
re-enable the check for up-to-date versions in the Tribble index.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4039 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-16 12:47:58 +00:00
37586d3a43
Don't exception out when bad aligners emit wonky alignments; instead, just don't clean
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4038 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-16 02:36:04 +00:00
a36951f11a
@output and @input arguments for table recalibration for use with Q
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4037 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-14 18:36:28 +00:00
61064d7075
GenotypeConcordance log file -- if provided, GC module will write FN/FP information to this file by context
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4036 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-14 18:35:57 +00:00
0d209d5442
Nicer printing out of clustering
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4035 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-14 16:02:13 +00:00
4710015c17
Disabled AlignerIntegrationTest while addressing build machine memory issues.
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2010-08-14 01:23:21 +00:00
307c8ca027
Created a new playground script for cleaning bams in Firehose.
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Some refactoring of Queue extensions for reusability in scripts.
Putting the extensions into the Queue.jar after building them.
More updates to GATK walker arguments specifying @Input and @Output for Queue.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4032 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 23:52:24 +00:00
dfe2922b5e
First working version of statistical haplotype phaser
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4031 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 21:29:45 +00:00
f36c0ed613
Stop building obsolete VCFTools and CGUtilities
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4030 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 19:28:36 +00:00
222f61df87
Bug fix for damoskow in TableRecalibration. Shouldn't try to update the reference mismatch rate tag for an unmapped read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4028 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 18:57:07 +00:00
80a70ccf03
Repopulating rodsToSamples. Code reviewed by Eric.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4027 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 17:07:18 +00:00
cb144734c0
Getting rid of GenotypeWriter interface. Of note:
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- GATKVCFWriter deleted, to be replaced if absolutely necessary when VCF writing goes into Tribble.
- VCFWriter is now an interface, for easier redirection.
- VCFWriterImpl fleshes out the VCFWriter interface.
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2010-08-13 16:33:22 +00:00
542d394e09
Cleaning up Queue debugging output.
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-l DEBUG with local programs now prints out the stdout/stderr of the programs as they are run.
More documentation in the examples with a new even simpler CountReads example.
Took out unused option to build Queue GATK extensions separately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4025 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 15:54:08 +00:00
49a3db9dfe
A brief implementation of a QD calculation that is not quite so bimodal for known variants (multiplicatively penalizes QD by (n variant samples)/(n variant alleles) ). Not sure how helpful this will be (which is why it is in oneoffs). Seems nice on MCKD1, but I'm still playing with the optimization.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4024 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 15:42:37 +00:00
c6a8fba922
Occasionally if a JEXL expression results in no variants being captured (like "QD > 20.0" on filtered variants) the per-sample mapping from samples to eval objects can be empty. This semi-hacky fix prevents null pointer exceptions in setting up the resulting empty table (by jumping straight to it in this case)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4023 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 15:37:45 +00:00
f874e548aa
Shame on us. FlagStat used ints instead of longs, so we ended up getting negative read counts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4022 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 03:00:57 +00:00
71c4d3f33d
Moving pointer to b36 reference from /broad/1KG to /humgen/1kg
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4021 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 00:54:34 +00:00
f39dce1082
Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).
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Added ability to skip up-to-date jobs where the outputs are older than the inputs.
Changed -T CountDuplicates --quiet to --quietLocus so that Queue GATK extensions can use both short and full argument names.
Short names can be used to set values on Queue GATK extensions, for example: vf.XL :+= myFile
Moved Hidden from the GATK to StingUtils.
Updated ivy from 2.0.0 to 2.2.0-rc1 to fix sha1 issue: http://bit.ly/aX72w7
Added Queue to javadoc and testing build targets.
Added first Queue unit test.
Another pass at avoiding cycles in the DAG thanks to all function I/O being files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4017 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 21:58:26 +00:00
8c08f47923
1) Make sure that the table size is set correctly in finalize()
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2) Make sure variants are biallelic before asking for isTransversion()
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4016 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 20:32:22 +00:00
41d57b7139
Massive cleanup of read filtering.
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- Eliminate reduncancy of filter application.
- Track filter metrics per-shard to facitate per merging.
- Flatten counting iterator hierarchy for easier debugging.
- Rename Reads class to ReadProperties and track it outside of the Sting iterators.
Note: because shards are currently tied so closely to reads and not the merged triplet of <reads,ref,RODs>, the metrics
classes are managed by the SAMDataSource when they should be managed by something more general. For now, we're hacking
the reads data source to manage the metrics; in the future, something more general should manage the metrics classes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4015 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 20:17:11 +00:00
7385cce494
Useful tool for calculating the perentage of misaligned reads at homozygous non-ref indel sites
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4013 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 17:57:44 +00:00
cc9e6b4ad9
Moved into Tribble to be with VC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4012 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 17:14:32 +00:00
14e492fa80
fix for a problem in readNextRecord() of BFS, where we'd go looking for the next record far into in the next contig because (f.getEnd() >= start) was never true once we cycled to a new conitg. Added a check for contig identity. Also, removed duplicate HW calculation classes in the GATK and Tribble.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4011 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 17:01:38 +00:00
cd4cd6db81
Added option to print out discordant sites in GenotypeConcordance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4006 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 19:55:19 +00:00
18fc5c8c3e
Initial implementation of annotator to compute allele balance for each sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4005 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 19:40:17 +00:00
1dc373b9d0
Initial implementation of evaluator to compute popgen theta statistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4004 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 19:36:34 +00:00
0a8ebcb4f9
moving tests over from the GATK to Tribble, and added a speed-up to the readNextRecord() that Mark suggested. Also removed the contained flag from the queries to Tribble in the GATK.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4003 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 17:54:59 +00:00
3ff6e3404e
Alleles are now returned in a consistent order, so we can deal with tri-allelic sites
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4002 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 15:21:10 +00:00
d514c424fd
adding tests for BTI in the ROD validation tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3997 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 06:05:40 +00:00
ca5b274f16
Unit, integration, and performance tests are all busted, so this is a good time to make a big commit...
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Major cleanup of the genotype writer code from the calling end. UG no longer supports making calls in anything but VCF, and that allows us to use the VCFWriter more generically now. Putting the ball in Matt's court to finish collapsing everything.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3996 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 04:18:29 +00:00
0f78f70ed4
fix for feature source in Tribble; we need to check that the record coming back isn't null. Also in the GATK added code to set the default logging level in integration tests to WARN, with the default level change they were spewing a bunch of text.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3995 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 02:57:23 +00:00
419a36f74c
Starting the clean up of the sting.utils.genotype code which is all either moving to Tribble, moving to sting.utils.vcf, or being removed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3994 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 02:16:05 +00:00
2a4a4b0aab
VariantRecalibrator now calls plot_Tranches directly so it works on the farm
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3993 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 23:17:16 +00:00
c2c0c1f57c
Removing used --enable_overlap_filters argument; Eric assures me this won't break the currently broken tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3992 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 22:27:13 +00:00
0f29f2ae3f
fixes for the Tree index, and some small clean-up in the GATK.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3991 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 20:41:50 +00:00
3eee3183fd
Checking in the tiger team changes. LOD calculation modified. -qScale is back in case people need it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3990 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 20:41:03 +00:00
0eeb659aa3
Useful utility function to print out the Allele as a String since toString prints out * for refs. It was annoying to keep seeing new String(Allele.getBases()).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3989 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 20:35:56 +00:00
d0ecb8875a
Added - a class to count functional annotations by sample (currently for the MAF annotation strings, soon to be migrated to genomic annotator once it is up and running)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3988 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 20:09:13 +00:00
5b0b9e79ba
protect against nulls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3987 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 19:21:39 +00:00
8944800f60
Minor refactoring for Ryan
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3986 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 18:05:23 +00:00
4f51a02dea
Changed logging level to default at INFO instead of WARN.
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Changes to StingUtils command line for use in Queue, replacing Queue's use of property files.
Updates to walkers used in existing QScripts to add @Input/@Output.
RMD used in @Required/@Allows now has a new default equal to "any" type.
New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions.
Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.)
Removed dependency on BroadCore by porting LSF job submitter to scala.
Ivy now pulls down module dependencies from maven.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3984 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 16:42:48 +00:00
30178c05c5
providing a way to specify how you'd like -BTI combined with your -L options; set BTIMR to either UNION (default) or INTERSECTION.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3983 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 14:00:52 +00:00
6b4a1e3b9f
Reenabling code that was commented out after it was confirmed to work by many participating in this thread:
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http://getsatisfaction.com/gsa/topics/error_thrown_when_reading_reference_file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3981 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 00:12:09 +00:00
48e311a5ea
Added copyright notice.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3980 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 07:11:51 +00:00
9aa70d9c7c
Replaced by SelectVariants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3979 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 07:07:42 +00:00
758ab428f5
Better logging info for the samples being selected and the sample expressions being ignored.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3978 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 07:03:37 +00:00
e242a8f143
Put single quotes around the regex. This isn't strictly necessary through the integration test machinery, but *is* necessary at the console, and it's convenient to be able to cut and paste this.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3977 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 05:56:57 +00:00
13f29660bb
Integration test for SelectVariants. Tests a complex case with an explicit sample selection, sample selection by regex, exclusion of non-variant and filtered loci, and JEXL selection on low allele-frequency variants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3976 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 05:49:47 +00:00
637a1e5055
Updating to use the new VA interface
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3975 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 05:31:01 +00:00
bd6d5a8d51
Adding command-line header to VA and VF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3974 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 05:21:15 +00:00
64446f0ddf
Avoid NaNs in the final output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3973 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 05:16:52 +00:00
3f6e44dc71
Updated recalibrator and cleaner to output full command-lines in the bam header
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3972 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 04:39:18 +00:00
0da0dfa1da
Cosmetic change - lower-case for all command-line arguments' short names.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3971 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 04:12:01 +00:00
eb1bb94d1c
Moved the evaluation of the JEXL expressions to a point *after* the samples are subset and the INFO-field annotations are updated. I think this makes more sense than having the evaluations happen beforehand, since it seems jarring to have the JEXL expressions operate on the annotations before they're updated, and have the file contain the annotations after they're updated. Now, selecting on something like allele frequency will actually apply to the annotations that actually end up in the file, while selection on other annotations (which are carried over without modification) will act exactly the same regardless.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3970 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 04:09:02 +00:00
594b7912f1
Added a generic method for returning the complete command-line used when calling a walker, to be used in the bam/vcf headers. As requested, every possible engine/walker argument is included. I've added it to the Unified Genotyper output, so people can try it out and let me know what they think. Something that needs to be discussed in group meeting: what happens when we merge VCFs? Do we keep all of the command-lines?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3969 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 03:53:07 +00:00
6e389059cf
An improved version of VariantSubset and VariantSelect, meant to replace those walkers. Takes in a VCF and creates a subsetted VCF by sample(s), JEXL expressions, or both.
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When subsetting by sample, the -SN argument is treated as a literal sample name and, if no match is found, as a regular expression. This allows for a large number of samples to be selected at once (useful when, for instance, cases are given one sample name prefix and controls are given another).
After the subsetting procedure, the INFO-field annotations AC, AN, AF, and DP are all recalculated to properly reflect the new contents of the VCF.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3968 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-08 02:57:06 +00:00
ac4699a650
Re-enabling this test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3962 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-06 20:20:37 +00:00
f275041b1c
-minimalVCF for CombineVariants. Work around for broken locking code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3960 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-06 16:10:59 +00:00
9076c0b28b
removing unused code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3958 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-06 14:24:39 +00:00
341e752c6c
1) AlleleBalance is no longer a standard annotation, but the Allelic Depth (AD) is for each sample.
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2) Small fixes in the VCFWriter:
a) Trailing missing values weren't being removed if their count was > 1 (e.g. ".,.")
b) We were handling key values that were Lists, but not Arrays. We now handle both.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3956 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-06 12:05:14 +00:00
c68625f055
Fixes from Mark for the MutableContexts; this fixes the clearGenotypes() and the clearFilters() methods, and adds a method to clear the attributes. Also added is a method for creating a variant context where the attribute list is pruned to a specific subset, which can be null.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3955 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-05 22:39:51 +00:00
72ae81c6de
VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:
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- Tribble is included directly in the GATK repo; those who have access to commit to Tribble can now directly commit from the GATK directory from Intellij; command line users can commit from
inside the tribble directory.
- Hapmap ROD now in Tribble; all mentions have been switched over.
- VariantContext does not know about GenomeLoc; use VariantContextUtils.getLocation(VariantContext vc) to get a genome loc.
- VariantContext.getSNPSubstitutionType is now in VariantContextUtils.
- This does not include the checked-in project files for Intellij; still running into issues with changes to the iml files being marked as changes by SVN
I'll send out an email to GSAMembers with some more details.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3954 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-05 18:47:53 +00:00
b21f90aee0
Added preliminary framework for performing short-range phasing (ReadBackedPhasingWalker.java)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3953 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-05 14:56:34 +00:00
a8d37da10b
Checking in everyone's changes to the variant recalibrator. We now calculate the variant quality score as a LOD score between the true and false hypothesis. Allele Count prior is changed to be (1 - 0.5^ac). Known prior breaks out HapMap sites
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3952 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-05 14:12:19 +00:00
07addf1187
Fix for Kiran: since the Variant Annotator will re-annotate on top of existing annotations it makes sense to remove old headers if they conflict with the definitions being added by VA.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3951 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-05 06:44:39 +00:00
1539791a04
Fix for Kiran: when using VCFs for the comp tracks in the Annotator(s), don't put the headers from them into the output VCF.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3950 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-05 04:45:47 +00:00
227c4b10f0
Bug fix for Chris: convert comp tracks to VC so that we can respect the filter field. Added an integration test to cover this.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3949 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-05 04:13:16 +00:00
84ca2f27bb
Bug fix for Chris: added method createPotentiallyInvalidGenomeLoc() to the GenomeLocParser that doesn't check that the contig exists in the sequence dictionary. This is crucial for lifting over from one reference to another, as sometimes contigs names change in the liftover (e.g. chrM to MT).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3948 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-05 03:19:02 +00:00
f247cbf68e
I want to be the first to use the new super-cool Hidden annotation! No more telling people not to use the cleaner debugging options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3947 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-05 02:44:37 +00:00
78bfe6ac48
Added @Hidden annotation, a way to deliberately exclude experimental fields and
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walkers from the help system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3946 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-05 02:26:46 +00:00
82d6c5073b
A simple read strand filter for potluri on get satisfaction
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3945 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 23:23:50 +00:00
d53d5ffbf6
A utility class that computes running average and standard deviation for a stream of numbers it is being fed with. Updates mean/stddev on the fly and does not cache the observations, so it uses no memory and also should be stable against overflow/loss of precision. Simple unit test is also provided (does *not* stress-test the engine with millions of numbers though).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3944 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 21:39:02 +00:00
8d8acc9fae
Moving G's MyHapScore to replace the old HapScore
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3943 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 21:00:54 +00:00
7858ffec32
Spit out the error in the warning message so that Sendu can tell me what his problem is
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3942 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 20:40:28 +00:00
86211b74e8
Bug fix: when padding alleles in creating a Variant context from an indel, leave no-call alleles as no-call alleles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3940 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 19:51:10 +00:00
38e65f6e1b
Added: A VariantEval module that gives simple metrics by sample, an an abstract class that makes per-sample modules easy to write (but a little bit clunky since a class needs be defined for each data point -- see SimpleMetricsBySample as an example). AnalysisModuleScanner needed a slight update to pull in data points from parent classes for this to work (thanks Khalid for showing me how to do this). After a code review with Aaron (thanks) and ensuring integration tests pass, I am committing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3939 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 19:37:39 +00:00
f13d52e427
Attempt to determine whether underlying filesystem supports file locking and
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disable on-the-fly dict and fai generation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3938 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 19:28:27 +00:00
340bd0e2c1
Removed hard-coded pointers to references
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3934 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 17:59:37 +00:00
a47824d680
A couple of type specific implementations of a single extend() method: takes an array (byte[] or short[] currently) and "extends" it to the left or to the right by the specified number of elements. Returns newly allocated array, with the content of original array copied in (if we extend by n elements to the left, then the returned array will have n default-filled elements *followed* by the content of the old array).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3932 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 15:30:48 +00:00
012a7cf0a5
mismatchCount now has a version that counts mismatches only along a part of the read (takes additional args start_on_read and length_on_read to specify the read's subsequence to be interrogated);
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isMateUnmapped() convenience shortcut method added.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3931 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 15:27:35 +00:00
e6e8a20a1e
1) Fix MyHaplotypeScore to ignore 454 reads, since all those pathological non-existing indels make some sites' score blow up. If a site is only covered by 454 reads, we (hopefully) detect this graciously and just emit a score of 0.0 for the site.
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2) New annotation SByDepth = log10(-StrandBias/Depth) (non-standard annotation, key name = "SBD"). If StrandBias/Depth happens to be positive (very rare but can happen), annotation gets value=-1000.
3) Abstracted out new class AnnotationByDepth so that QD and SBD can share code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3930 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 15:23:08 +00:00
bf60ed0b25
Needed it here too: warn user instead of dying if the R script cannot be executed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3929 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 13:11:27 +00:00
40ffe34686
Warn user instead of dying if the R script cannot be executed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3928 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 13:08:15 +00:00
17d5e89734
Now --list annotates which modules are Standard
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3927 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-03 21:00:37 +00:00
72875cf717
Removing annoying printouts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3926 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-03 19:55:00 +00:00
2307bed742
VariantEval now uses the "standard" modules only by default. You can add other modules with the -E argument and not use all of the standard ones with -noStandard (they can be added back individually with -E).
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Generalized some of the packaging code from VariantAnnotator. Matt might want to take a look to make this nicer...?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3925 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-03 16:51:10 +00:00
a7ff9caf54
Added sanity check against bad people and/or crazy big indels at edges of ref context
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3918 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-03 05:37:17 +00:00
5f1b67c1de
Coping out and forcing the entire GATK (and associated JVM) to use US English
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locale. Method to force JVM into proper locale exists in CommandLineProgram
and is disabled by default, but implementers of CommandLineProgram can opt in
to the forced US locale by calling a static method.
Question for the VCF developers: I removed the code to explicitly output doubles
in US locale. Do you / how do you want to handle this in applications that use
Tribble outside the GATK?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3917 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-03 03:48:26 +00:00
2bc69572cb
Make transcript2info capable of handling b37/hg19 contigs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3915 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-02 17:32:08 +00:00
c203e0fb02
Added JEXL support for hetCount, homRefCount, and homVarCount in VCs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3914 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-02 12:24:11 +00:00
7fab5c0a8f
support for -singleton_fp_rate arguments to variant recalibrator instead of the pop.gen. AF prior. Worth experimenting with Ryan.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3913 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-31 21:17:47 +00:00
6d91cd587e
Be explicitly clear about which options are for debugging purposes only and shouldn't be used if your username is not ebanks@broad. If only we had a @hidden annotation option for args...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3909 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-30 14:18:31 +00:00
ac8048f17b
Support for automated selects for tranches in variant eval -- use -tf to make tranch-specific ve outputs. ApplyVariantCuts with tranche reading functions for general use, along with todo for ryan. CombineVariants now has --filteredAreUncalled and will treat filtered snps in input VCFs are uncalled, and so won't emit -filteredInOther set features
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3908 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-30 14:16:43 +00:00
9231d13252
Minor modification: adding an argument to make slightly more general.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3907 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-30 05:20:20 +00:00
db54d63fc7
Hahaha yes, ownage. This now works.
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BTW, Eric, thanks for forwarding the DepthOfCoverage thread to gsamembers. I'd forgotten about reduce by interval. Mighty helpful in this case!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3906 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-30 04:23:02 +00:00
3e3f8c7692
Simple count intervals walker, as per my recent email to GSAMembers. Never use this. It doesn't behave the way you think it does.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3905 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-30 03:39:23 +00:00
ba1a330293
Corrected location and made more explicit the error message thrown if someone tries to read a VCF 3.3 file with indels, which is not supported.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3901 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 20:02:47 +00:00
5af986e0c1
Add an integration test for Beagle (one for ProduceBeagleInput and one for BeagleOutputToVCFWalker)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3897 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 18:49:22 +00:00
e1a34685fd
Add back MyHaplotypeScore as a new implementation for HaplotypeScore, this time as a non-standard annotation. Implementaiton is also better, it computes better consensus haplotypes, ranks them by sum of quality score.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3890 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 21:23:19 +00:00
6c93b13428
A Java sizeof, implemented using the Java instrumentation API. Can either get the memory consumed either only by a single
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object or by a single object and all the references it contains. Requires a command-line change to add a Java agent to
the command-line; see the Sizeof.java javadoc for details.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3889 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 18:44:15 +00:00
f5566a6593
Knocking out some quick findBugs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3887 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 14:10:59 +00:00
894623858d
OK, bad idea to add new temporary annotation - revert to keep integration tests hapy.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3886 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 12:07:13 +00:00
71bfb1ee35
First redesign of HaplotypeScore - now, a different approach is taken to build possible haplotypes at a site: first, all possible haplotypes consistent with reads are formed (reference is not used). After this list has been formed, it is ranked according to the number of reads that are consistent with it and the two most popular haplotypes are chosen.
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this reduces to the old method in typical cases, but it builds haplotypes correctly if there are two variants close by within a context window.
Annotation is temporarily named MyHaplotypeScore so it can be run in parallel with old one, soon it will be renamed after some more testing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3885 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 10:54:56 +00:00
cffebcc867
Small utility walker used for production of the Beagle data processing paper section. Walker will print out to output file, for every site common to a reference vcf and an eval vcf, a given sample's depth, hapmap AC and AF and pre/post Beagle genotype as well as corresponding reference (e.g. Hapmap) genotype.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3884 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 03:00:17 +00:00
1d9ed1e214
Cleanup of old VCFRecord code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3883 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 02:56:47 +00:00
7dd55fbf13
Archiving
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3882 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 02:47:18 +00:00
9667942e52
fix for Ryan's issue: we also need to sync when we store a resource.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3881 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-26 22:17:47 +00:00
8b072b59e2
Returning index dumping functionality in BAMFileStat to a useable state.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3880 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-26 20:03:50 +00:00
19ad44d332
Minor improvements to CombineVariants to handle the complex case from Chris. IntegrationTest of complex case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3876 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-25 13:46:11 +00:00
7c5a3836db
Trivial changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3875 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-25 04:00:47 +00:00
56de475f11
Based on feedback from non-GSA users, who claim that our exceptions are 'scary and overwhelming,' I've cleaned up the error message to first describe the error and what users should do and then ask them to copy the subsequent stack trace into their GetSatisfaction posting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3874 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-25 03:57:44 +00:00
9bd8a2685b
Because the performance tests were busted on LSF, no one caught this error until now: when Matt changed over the contract for the AlignmentContext, this line needed to get updated too. All is well now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3873 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-25 02:53:01 +00:00
b551eaf8fd
Actually commit the code that makes variant eval run in a reasonable amount of time.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3872 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-24 17:32:03 +00:00
b0b37c3476
No handles (I believe) reference only VCs correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3871 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 23:09:23 +00:00
e21376219d
Updates to CombineVariants for Tim. -setKey can be null. Integrationtests for -setKey foo and -setKey null.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3870 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 22:35:52 +00:00
26bb1cd9ce
Fix broken test correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3869 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 20:47:41 +00:00
4fc1db7aaf
Change interface to VCFWriter add() method to take only 1 byte from reference (since that's the only thing it needs), to prevent bugs like having people call it with ref.addBases() which is wrong (since it provides bases starting from the left of reference context window).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3868 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 20:24:03 +00:00
b3fd145161
fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no
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features in that contig. Thanks to Mark for finding this. I'm not rev'ing the index version (which would cause all indexes to be rebuilt), since this seems like a pretty rare edge case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3865 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 18:39:55 +00:00
33090629ea
VariantEval can now see the EvaluationContext group objects, so they can decide if/when to print interesting sites. GenotypeConcordance has a hard-coded option to print FNs that is on the way to being generally useful. VCFWriter now uses the US locale for formatting floating point numbers; I believe this fixes a long-standing annoyance. Italian guys will check on this.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3864 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 17:16:50 +00:00
5eef15cfdf
a) Bad bug fix to CombineVariants: when indels were being merged, the reference base provided was wrong - ref.getBases()[0] was being used, but this returns bease at start of window. Instead, the reference at current locus should be used.
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b) Cosmetic change to Beagle annotation description.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3861 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 15:13:47 +00:00
4ff8b8fc0e
1. Fixing a bug that Mark found where indel-containing clipped reads would get an original cigar tag even when they didn't actually get modified.
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2. Added some useful logging messages.
3. Added a oneoffs walker to calculate the number of realigned reads and intervals containing them.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3860 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 14:24:01 +00:00
973934f769
Depth of coverage now uses longs rather than ints. We can now successfully run on the Lepidosiren paradoxa genome. (about 80 GB)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3859 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 14:14:12 +00:00
536399eaa0
Improvements to variant combine. Now calculates AC/AN/AF correctly by calling into the VariantAnnotator engine. Automatically removes annotations that are inconsistent across incoming VCs (in simpleMerge). TODO bug fix for Guillermo/Eric.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3858 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 13:33:11 +00:00
9579aace1f
updates to code dependent on Tribble, as well as the following Tribble changes:
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- makes writing to disk optional for indexes using the indexCreator classes (allow the user to specify the index file, if null don't write it)
- removed some system.out debugging code
- fixed version checking in interval tree
- made indexes store and return a LinkedHashSet for sequence names (to ensure they've preserved the ordering in the file)
- index creators now read the file before creating the index
- changed the Index.write() method to take a LEDataStream instead of a file
- removed the sequence dictionary code on the header
- added utils for getting LEDataStreams
- added a base Tribble exception
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3857 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 01:56:10 +00:00
c5325b03be
1) Removed hard-coded strings. Please let's use the fields defined in VCFConstants.
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2) General code cleanup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3856 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 01:49:47 +00:00
e9d243babb
More improvements to exception handling during multithreaded runs based on
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a bug reported by Ryan.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3855 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-22 22:13:01 +00:00
83798225ac
Repackaged datasource-specific command-line tools into their own package. Added a tag renamer tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3854 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-22 19:50:34 +00:00
98caedb5f0
Forgot to update VCF4 unit test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3853 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-22 16:25:51 +00:00
485023ba8e
this.intersect(that) method added to GenomeLoc (returns intersection of two intervals or dies if the locations do not overlap)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3852 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-22 16:00:30 +00:00
3308d956f4
Added utility shortcut method: getOriginalQualsInCycleOrder(read)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3851 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-22 15:44:25 +00:00
473ec91633
a) Bug fix in VCFHeader parsing - Info fields were not being parsed properly, with the result that the Count field was not being properly displayed in records (e.g. if Count=0 for a particular field, the INFO tag was still being displayed as ...;Field=x;... instead of ...;Field;...
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b) Bug fixes and update to how we represent indels and other complex events in a VariantContext object. Convention is now that all events are left aligned, with the first variant context location marking the common base before an event occurs. However, alleles in a VC don't have the common base in all VC's. Two new functions are now part of VariantContextUtils: CreateVariantContextWithPaddedAlleles and CreateVariantContextWithTrimmedAlleles. Both take a VC as an input and create a VC as an output.
Main flow is that a VCF reader would create a VC with trimmed alleles, all walkers would ideally work with these trimmed alleles, and then the VCF writer would pad back the alleles before writing. However, there are special cases where we need to pad alleles like for example when merging/combining VC's.
Pending issues:
- PED and DBSNP RODs have to be updated to create VC's for indels following the convention above. Changes will go in after Tribble location is moved and things are tested.
- Need to verify Indel genotyper and other modules that create VC's with indels.- Wiki page describing convention above and how walkers should interpret indel VC's still needs updating/detailing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3850 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-22 02:36:45 +00:00
b696c3ea98
No more traversal reduce results.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3849 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-21 18:34:54 +00:00
365b42390d
Support for generating (very basic) wiggle files for use with IGV (see UCSC for wiggle spec); and a walker to take in a variant track and create a transition transversion rate track for the whole genome (due to the wiggle spec, this has to be done by chromosome). It's interesting to see the effect of genes!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3848 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-21 18:04:30 +00:00
f7957bc7f2
Fixed memory leak in VariantEval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3845 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-21 12:35:46 +00:00
1cba81c16f
updates to tribble with fixes for some bugs I've found in some new indexing code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3842 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-20 22:08:04 +00:00
ff6748d1cd
oops - missed one
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3841 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-20 18:55:19 +00:00
c6ad26e04f
1) When quals/GQs are really integers (x.00), strip off the floating points.
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2) Keep track of whether vcf records are unfiltered vs. pass filters in the variant context so we can regenerate the records on output.
3) No more "ID" hard-coded all over the code to set the VariantContext ID. Use a static variable instead.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3840 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-20 18:01:45 +00:00
0db7fab1a9
Fixing genotype filtering for VF and adding integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3839 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-20 07:30:21 +00:00
2a6c2d3098
re-enable test; I was moving the input file in prep for my last commit around on Eric, so he rightfully removed the test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3838 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-20 07:14:59 +00:00
0108517b98
updating the Tribble track loading code to use the new shared locks, updated lots of new tests, add infrastructure for the TreeInterval, and removed the old locking class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3837 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-20 07:08:10 +00:00
f742980864
1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon.
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2. Moved Jared's VCFTool code into archive so that everything would compile.
3. Added the vcf reference base (needed for indels) as an attribute to the VariantContext from the reader.
4. TribbleRMDTrackBuilderUnitTest was complaining that a validation file didn'r exist, so I commented it out.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3835 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-20 06:16:45 +00:00
70b07206a2
CombineVariants tests for Guillermo and Eric to explore the correctness of the in/out reader, writer behavior of the system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3834 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-19 22:41:48 +00:00
c47a5ff5ab
Official parallel CountCovariates, passes all integration tests. Now poster-child example of parallelism in GATK (Matt H). Apparent general performance improvements throughout too.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3833 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-19 22:13:18 +00:00
0b56003d1a
Remove stray commented out line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3832 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-19 19:14:39 +00:00
8e31c01680
Solid processing in base quality recalibrator now has several options for how to handle no calls in the color space. --ignore_nocall_colorspace is removed and replace by --solid_nocall_strategy. Fixed some of the @Deprecated tags in BaseUtils. LocusWalkers now filter out FailsVendorQualityCheck reads. HLA caller integration test bam file had bad vendor reads so its integration test changed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3831 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-19 19:10:29 +00:00
18b0114e25
remove FixBAMSortOrder walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3830 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-19 17:27:23 +00:00
f4cfb0f990
The first step in integrating Jim's tree based index scheme:
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- changed to a better method for getting headers from Codecs
- some removal of old commented out code in the GATKAgrumentCollection
- changes for the rename of FeatureReader to FeatureSource
- removed the old Beagle ROD
- cleaned up some of the code in SampleUtils
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3826 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-19 04:49:27 +00:00
40a963541d
Uniquify the registered MXBean by adding an instanceNumber=... tag to the
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ObjectName. In the Queue-enabled future, we might want to come up with GUIDs
(or at least semi-unique IDs) so that we could use JMX to track runtime
attributes for multiple jobs running simultaneously.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3825 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-19 00:58:54 +00:00
5a1a3fc79a
Fix bad VariantContext creation in unit test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3824 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-18 20:21:01 +00:00
7c42e6994f
FindBugs fixes throughout the code base
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3823 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-18 16:29:59 +00:00
693672a461
Refactoring the VCF writer code; now no longer uses VCFRecord or any of its related classes, instead writing directly to the writer. Integration tests pass, but some are actually broken and will be fixed this week.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3822 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-18 13:19:56 +00:00
379584f1bf
Re-enable (most of) these tests. Guillermo will re-enable the other one when the VCF->VC conversion is done for indels
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3821 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-18 03:24:28 +00:00
982947d328
update to deal with partial indels (I/D with no bases) in the HM records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3820 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-18 02:56:37 +00:00
414ec6f20a
Removing version argument constructors that shouldn't be used. Temporary allow -- with global variant to indicate this should be removed -- header records without description fields. Real error checking in the headers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3818 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-17 22:30:08 +00:00
14b21e487b
always 4.0
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3817 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-17 22:28:48 +00:00
d40299840c
indenting clean up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3816 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-17 22:28:28 +00:00
9207c58b8f
A fix for the integration test I broke on Friday on my way out the door --
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some workflows using AlignmentContext were working with it in a way I didn't
expect and wound up treating extended pileups as base pileups. I'll work to
make sure the AlignmentContext interface is crystal clear.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3815 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-17 22:22:44 +00:00
55b756f1cc
First step in major cleanup/redo of VCF functionality. Specifically, now:
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a) VCF track name can work again with 3.3 or 4.0 VCF's when specifying -B name,VCF,file. Code will read header and parse automatically the version.
b) Old VCF codec is deprecated. Reader goes now direct from parsing VCF lines into producing VariantContext objects, with no intermediate VCF records. If anyone can't resist the urge to still input files using the old method, a new VCF3Codec is in place with the old code, but it will be eventually deleted.
c) VCF headers and VCF info fields no longer keep track of the version. They are parsed into an internal representation and will be output only in VCF4.0 format.
d) As a consequence, the existing GATK bug where files are produced with VCF4 body but VCF3.3 headers is solved.
e) Several VCF 4.0 writer bugs are now solved.
f) Integration test MD5's are changed, mostly because of corrected VCF4.0 headers and because validation data mostly uses now VCF4.0.
g) Several VCF files in the ValidationData/ directory have been converted to VCF 4.0 format. I kept the old versions, and the new versions have a .vcf4 extension.
Pending issues:
a) We are still not dealing with indels consistently or correctly when representing them. This will be a second part of the changes.
b) The VCF writer doesn't use VCFRecord but it does still use a lot of leftovers like VCFGenotypeEncoding, VCFGenotypeRecord, etc. This needs to be simplified and cleaned.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3813 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 22:49:16 +00:00
75bea4881a
Modified SampleFilter to allow for multiple samples to be given. AminoAcidTransition now turns on when you give VariantEval the right commands.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3812 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 21:27:32 +00:00
36ac73cf9a
comment out broken test until it can be fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3810 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 20:04:40 +00:00
96034aee0e
Cleanup for Steve Hershman's issue. In the midst of doing this, I discovered
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that the semantics for which reads are in an extended event pileup are not
clear at this point. Eric and I have planned a future clarification for this
and the two of us will discuss who will implement this clarification and when
it'll happen.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3809 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 18:57:58 +00:00
6aedede7f3
Added Type.MNP to allowed variant context types; this does not break the tests (yet)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3808 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 15:50:25 +00:00
1dd8a28a5d
Added new query: isMNP(feature); returns true if dbsnp feature is multi-nucleotide polymorfism (e.g. a di-nuc TA ->CC)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3806 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 15:32:10 +00:00
ec94cfdf05
remove unit test for VCF writer, it's not applicable now that we produce only VCF4. Guillermo, it's up to you if you want to adapt this or remove it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3803 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 14:33:25 +00:00
b29eda83bb
Parallelized CountCovarites! percent_ref_called_var now a standard genotype concordance module (for validation!). Really much smarter merging of headers for combineVariants. VCF codecs now actually look at the file version and blow up if they are the wrong versions. setHeaderVersion() in VCFHeaderLine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3802 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 14:10:18 +00:00
f293eb7de1
Fix for Kim: for some ungodly reason, I was initializing the bins that were maintaining counts to 1 instead of 0.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3801 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 03:40:29 +00:00
e7e58d7129
The SAM spec has now officially reserved my new tags for original cigar and original alignment start... except that OS has been named OP ('original POS')
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3800 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 00:09:36 +00:00
ab84ed8c68
Fix for Mark: get rid of old program tags whose IDs clash with the recalibrator/realigner tag (including if the id has a .1 at the end, etc.). Keeping them around is dangerous because we don't know which one refers to the latest run of the tool on the bam.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3798 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-15 19:13:50 +00:00
dfddf8fd75
- Bring the PaperGenotyper up to code.
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- Remove some old debugging cruft regarding handling of threaded engine exceptions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3796 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 22:31:21 +00:00
f65cba6b9a
Adding support for shared file locking via a new class for file locking, FSLockWithShared. This will eventually take over for FSLock, the current file locking class - I'll work with Aaron to merge the tribble code that uses FSLock right now.
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FYI: creating an exclusive lock on a file that does not exist will create that file as an empty file, and will NOT delete that file after the program terminates. So watch out if it's possible that the file you're locking does not exist - could end up leaving extra files that confuse users.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3795 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 20:45:51 +00:00
a8caa20378
Previously the hierarchical microscheduler defensively coded around and reported exceptions of
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the walker itself, but didn't do a great job of catching framework exceptions. This became extremely
unfortunate in the case where walkers caused exceptions that manifested themselves in the framework,
such as when the walker opens more files than file handles are available.
Reworked the exception handling so that framework errors are treated like walker errors and the resulting
exception bubbles out of the walker. Stack traces for threaded walkers are still convoluted and nasty.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3794 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 20:34:43 +00:00
bf384f48e1
Reverting previous change because it won't always work. More investigation needed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3793 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 19:13:17 +00:00
e4bfb06888
Check header type instead of rod type, since rod type will now be VC and not VCF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3792 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 19:10:09 +00:00
0226412b11
Add GQ to list of genotype attributes for reg exp
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3791 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 19:01:11 +00:00
78a4d8ec3d
Removing more references to VCFRecord
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3790 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 16:34:15 +00:00
af23762778
Removing more references to VCFRecord
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3789 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 11:54:23 +00:00
a4f8d70d8d
oops, forgot to update this integration test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3788 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 11:38:33 +00:00
460283f6d2
No more manually converting VariantContexts to VCFRecords. You should be utilizing VCs and not VCFRecords.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3787 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 05:21:28 +00:00
6b5c88d4d6
The GATK no longer writes vcf3.3; welcome to the world of vcf4.0. Needed to fix a few output bugs to get this to work, but it's looking great. Much more still to come. Guillermo: hopefully this doesn't break your local build too badly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3786 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 04:56:58 +00:00
9d2a485532
Update to AminoAcidTransition eval module
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3783 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-13 17:12:03 +00:00
3db7fbb5e9
Fix for added EOF in csv file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3781 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-13 16:09:48 +00:00
9a05e8143d
Move to 4.0 and away from VCFRecord.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3780 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-13 15:54:54 +00:00
6442dabf94
Deleting/archiving as instructed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3779 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-13 15:23:50 +00:00
7e7da75d27
Moving over to 4.0 and away from VCFRecord
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3778 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-13 14:07:10 +00:00
d896d03554
Moving VF to vcf 4.0. Still need to fix genotype filters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3777 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-13 11:39:51 +00:00
76b3b39720
Technically, Mark broke this with his commit earlier. But since I had an outstanding broken test, I lose and have to fix this one too...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3776 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-13 03:58:38 +00:00
1bef7dd170
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3775 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-13 00:56:12 +00:00
de969f7cc7
logger != null check
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3774 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 23:07:14 +00:00
2e445262f2
Promotion to . for variable numbers of arguments
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3773 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 22:53:53 +00:00
297f15a60c
Protect ProduceBeagleInputWalker against evil users who feed to it VCF's with indels, no variation sites or other interesting markers: Write to Beagle input only in biallelic SNP sites since that's the only thing Beagle can do.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3772 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 20:54:42 +00:00
52c534a8f2
Updating to VCF 4.0
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3770 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 20:18:30 +00:00
5992b79159
a) Simplify normalization code in ProduceBeagleInputWalker, as to always normalize, and use MathUtils.normalizeFromLog10 to do this.
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b) Several improvements to BeagleOutputToVCFWalker:
1. If a Hapmap input track is provided (e.g. -B comp,VCF,file), Hapmap sites will be annotated with Hapmap Allele count and allele frequency (key ACH, AFH).
2. If probability of correct genotype is lower than ncthr (optional argument provided by user, default = 0.0), walker will keep original calls instead of using Beagle calls.
3. Instead of annotating just whether Beagle had modified a site, annotate instead HOW MANY genotypes in a site were actually changed by Beagle.
All three improvements are mostly for debugging and analysis only.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3769 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 19:54:58 +00:00
e50627a49e
1. Updated tests and added integration test for liftover code.
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2. Updated liftover code (and scripts) to emit vcf 4.0 and no longer depend on VCFRecord.
3. Beagle walker now also emits vcf 4.0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3767 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 17:58:18 +00:00
2a7112302a
More archiving
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3766 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 17:04:41 +00:00
221e01fb27
deleting/archiving as instructed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3765 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 16:59:45 +00:00
8086ab1f75
Pulled sample/header merging routines out of CombineVariants and into util classes. Added more generalized methods for retrieving samples. Updated the Beagle walkers to use these methods.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3764 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 16:51:54 +00:00
0c4a32843c
No longer uses VCFRecord
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3763 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 13:57:39 +00:00
f130d29318
No longer uses VCFRecord.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3762 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 13:34:10 +00:00
e75b3e13bd
updating unit test for previous fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3761 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 03:23:53 +00:00
0427f3554b
Bug fix: valid fields were being stripped off the FORMAT for samples because String.match was used instead of String.equals. Also, please use VCFConstants from now on instead of hard-coding e.g. missing values into the code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3760 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 03:06:51 +00:00
fb717fe128
First pass needed to remove old VCF code: moving all VCF-related constants into a single unified class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3759 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-11 07:19:16 +00:00
6b960bd9c5
Fix for Steve: genotype filters still want to see the values from the VC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3758 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-11 04:30:15 +00:00
c3c66e853c
Improvements for Jason
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3756 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 20:18:37 +00:00
405be230d0
Various code improvements based on FindBugs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3755 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 15:04:48 +00:00
abaec13e38
Bug fix: if there are samples in the VCF but all of them are no-calls, we still need to emit GT for the FORMAT field to be on spec. Note that this is a holdover from 3.3 writing but can't easily be fixed there. Fortunately, that code is all going away soon...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3754 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 14:08:25 +00:00
ea8fd506bf
Update to PickSequenomProbes: Option to ignore mask sites within X bp of a variant (very useful for indels where dbSNP entries near the indel are almost always false SNP calls). Also fixed an integration test where the variant site itself, being in dbSNP, was represented as [N/C] rather than [A/C]. Added integration test for 1bp no-mask window.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3753 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 04:03:19 +00:00
179067e3f4
Support for . values in qual field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3752 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 01:47:02 +00:00
45fb614296
Fixes to VE for obscure bug, as well as disabled integration test for CombineVariants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3749 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 00:13:07 +00:00
67f1589652
--fdr_filter_level isn't mandatory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3748 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 22:48:30 +00:00
5d39cd5db8
Added --fdr_filter_level to ApplyVariantCuts so that you can create beautiful tranche plots and also decide which tranche level to filter at. The previous version always filtered at the smallest tranche. The tranche filter names are appropriately added to the VCF header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3747 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 22:44:10 +00:00
760aaeda88
Update to CombineVariants. Now splits merge options into variant and genotype options separately.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3746 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 20:09:48 +00:00
bd2ba3eb37
deal with very large known indels that fall off our ref context
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3745 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 20:05:16 +00:00
12fecc8d8f
remove the picard DbSNP ROD.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3743 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 17:46:00 +00:00
56a0c7ee6f
All headers are now converted to VCF4 by default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3741 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 14:14:17 +00:00
6e6ad36523
reallow MNP events through
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3740 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 06:26:52 +00:00
ed0d0d78fa
corresponding fix for dealing with insertions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3739 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 05:25:03 +00:00
ada8c9931f
We were never clipping the VCF-provided ref base off the left end of the alleles for insertions, so the reference allele was never null (and downstream walkers would fail). Didn't this get tested with insertions at some point?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3738 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 05:24:27 +00:00
9a81f1d7ef
Fixed this tool for chartl so that it now properly handles deletions. Added deletion case to integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3737 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 04:45:59 +00:00
47a42b1507
trivial cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3736 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 04:42:32 +00:00
b7a3d1e61f
Bug fix: if the FORMAT field consisted of just GT, we were exceptioning out. How did we not catch this until now?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3735 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 04:41:40 +00:00
1c146aebe8
Fix logic bug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3734 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 04:32:46 +00:00
9fc05ac2ae
eagerDecode is now false.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3733 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 22:51:48 +00:00
4bc3ad2194
Shame on me: UG was emitting negative QUALs (-0) in all_bases mode. Thanks, Matt.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3732 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 20:30:22 +00:00
30714ec8d9
As per quick chat with Richard Durban, don't increase the mapping quality of realigned reads too much; for now, arbitrarily increase the MQ by 10. We need to figure out a better solution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3731 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 20:12:59 +00:00
8ff1a4b929
Don't try to clean reads that fail the PF, in preparation for Ryan
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3730 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 19:49:36 +00:00
b934cc7554
Updates to fix some bugs in merger. Now able to merge into project wide indel VCF files. Integration teests coming tomorrow
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3727 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 03:16:33 +00:00
7be8c35eb2
Workaround for scala trait erasing parameterized types:
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- Requiring explicit @ClassType on parameterized fields in traits.
- Scatter / Gather functions are now abstract classes since @ClassType can't be used on parameterized fields with type parameters.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3726 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 03:15:10 +00:00
120f90da5b
Interval support for ref walkers while streaming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3725 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 03:14:59 +00:00
773a72e6ea
An initial fix for performance issues when filtering UG with new StratifiedAlignmentContext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3724 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 01:07:46 +00:00
be75b087ec
a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype.
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b) Add "OG" annotation to genotypes. If Beagle changes genotypes, this annotation gets the original genotype call, to ease performance comparisons. If not, this annotation gets an empty value.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3723 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-06 18:33:28 +00:00
4213e05aeb
Fix for sharding ref walkers via monolithic sharding. Introduces the potential bug (for
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monolithic sharding only) that when traversing by read, map() function will not be called for loci
off the end of the reference.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3722 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-06 04:34:38 +00:00
86031f4034
part two: todo's in combine variants, fixes for InferredGeneticContext, and some other tests and clean-up.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3721 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-05 21:07:53 +00:00
36edc60ccc
Connected UG to the new comp track annotation system in VA. Also, when emit confidence is lower than call confidence (so that we emit records filtered with LowQual), add a corresponding FILTER header field to the VCF so that the validator doesn't complain.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3720 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-05 13:04:24 +00:00
3347d1ca7c
part one of combining format and info header lines code into a single abstract class for Mark; plus some 'm' removals from access methods for Eric. Adding fixes for CombineVariants next.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3719 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-05 05:57:58 +00:00
e7220bc885
Variant Context simple merging routine should keep ID if one of the VCs has it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3718 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-05 01:10:15 +00:00
3016e1cf80
Fixes to increase robustness in vcf4 writer. We assume that only at most 1 base was clipped from beginning of allele encoding by reader, and improve the way we find if bases were clipped. We still cant deal with some corner cases, and duplicate records may follow, for example if a snp location is followed at the next base by an indel. Also, if we are reading form a 3.3 vcf and the reference is null (ie we have an insertion), the reference base is not computed correctly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3717 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-04 20:22:04 +00:00
07945040f8
Set VariantFiltration's JEXL engine to silent for warning messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3716 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-04 18:11:19 +00:00
be8740b00d
Another edge case in left alignment for indels: deal with cases when insertions are ambiguously placed at ends of reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3715 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-04 17:26:38 +00:00
rpoplin
depristo
chartl
aaron
ebanks
fromer
kiran
delangel
hanna
asivache
kshakir
corin
flannick
bthomas