cd5d42618f
Killing old version of ivy jar.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4018 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-12 01:32:03 +00:00
f39dce1082
Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).
...
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()
...
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.
...
- 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
86bd55408e
no INFO output now that it's the default
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4014 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 18:56:28 +00:00
7385cce494
Useful tool for calculating the perentage of misaligned reads at homozygous non-ref indel sites
...
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
...
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.
...
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
e0abb73fd7
plot now assumes 1 / 1000 is the min error rate, not 1/100
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4010 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 14:48:22 +00:00
6037443e55
Handle interactive and non-interactive modes more elegantly.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4009 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 02:38:53 +00:00
a7409df1a6
Be more robust to missing or empty files in VariantEval output.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4008 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 02:22:50 +00:00
23b5d71e76
A quickly hacked together replacement for AnnotateVCFwithMAF.py, which doesn't work anymore with Cancer's updated annotator. Takes an annotated MAF file and imports the annotations into the VCF file. For the MAF annotator's DNP and TNP annotations (which I think are likely to not be correct, given the lack of phasing information or even proper association to the same sample), just propagate the annotation from the previous annotated variant to which the multinucleotide polymorphism was associated.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4007 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 00:20:08 +00:00
cd4cd6db81
Added option to print out discordant sites in GenotypeConcordance
...
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
...
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
...
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.
...
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
...
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
67063deb16
Removed coloring by mixture weight. Each cluster gets a distinct color, and the legend indicates which cluster has which id and its weight
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4001 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 14:28:24 +00:00
672bee295c
now plots tranches separately from optimizer
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4000 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 12:02:52 +00:00
cd2d051209
full path to Rscript
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3999 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 12:02:38 +00:00
9b432d0801
1kg script now works
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3998 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 12:01:18 +00:00
d514c424fd
adding tests for BTI in the ROD validation tests
...
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...
...
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.
...
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.
...
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
...
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
...
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.
...
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.
...
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()).
...
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)
...
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
...
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
...
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
c66e93d86e
Fixed a problem when mixing queue with other targets, such as 'ant clean oneoffs queue' and the STING_BUILD_TYPE environment is set.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3985 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 17:59:51 +00:00
4f51a02dea
Changed logging level to default at INFO instead of WARN.
...
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.
...
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
f3883585d0
removing the build lines I inadvertently committed. As a note: these are the lines you need to add if you want to debug tests, just don't check them in.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3982 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 13:48:16 +00:00
6b4a1e3b9f
Reenabling code that was commented out after it was confirmed to work by many participating in this thread:
...
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.
...
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
...
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.
...
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.
...
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
...
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
...
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
...
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.
...
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
...
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.
...
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.
...
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?
...
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
kshakir
chartl
hanna
ebanks
aaron
depristo
kiran
flannick
rpoplin