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
9ec393bfce
Updated md5 - vcf header line change
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3714 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-02 21:02:09 +00:00
f7593435eb
Implemented decodeLoc(..)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3713 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-02 21:01:36 +00:00
cd2e4b0a1e
merging now very close to working. Bug todo in writer and vcf infrastructure. Can almost create merged snp and indel files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3712 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-02 20:09:25 +00:00
b6bdd61283
a) Fix bug when multi-base reference is homopolymeric when writing a VCF4.0 variant context: computation of number of trailing bases was incorrect and we ended up with incorrect position.
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b) Updated VCF4WriterTestWalker to take either VCF3 or VCF4 as inputs (this walker can also be used to convert from 3.3 to 4.0).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3711 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-02 15:19:42 +00:00
61e2b2e39b
Nearly finalize merging capabilities for CombineVariants. Support for dealing with inconsistent indel alleles at loci. Improvements to Allele and removal of addAllele to MutableGenotype. We are close to being able to merge all of 1000 genomes -- snps and indels -- into a single combined vcf
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3710 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-02 13:32:33 +00:00
cab8394103
The sharding system now buffers reads, with a size determined by command-line argument. Will investigate whether/how this
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impacts performance on low-pass data and, if it works well, will create a more automatic version of the tool.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3709 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 22:28:55 +00:00
f967cae1aa
tiny comment change
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3708 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 22:04:25 +00:00
3093a20a55
fixing VCF header format and info fields so that they propery emit the unbounded count value correctly for vcf4 or vcf3. Eric we should update the vcf4 spec page to indicate format fields are allowed to use the unbounded count as well (if this is true).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3707 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 22:02:16 +00:00
61c07c6f90
Fixes for missing key values that can create null pointer exceptions when reading from 3.3-generated variant contexts. Also, chop missing genotype fields correctly from right to left
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3706 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 20:17:03 +00:00
255b036fb5
Variant Recalibrator MLE EM algorithm is moved over to variational Bayes EM in order to eliminate problems with singularities when clustering in higher than two dimensions. Because of this there is no longer a number of Gaussians parameter. Wiki will be updated shortly with new recommended command.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3704 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 18:51:07 +00:00
4903d1fb4f
fix for a parallelization issue: moving the creation of iterators outside of the sync block so we don't wait for RMD tracks to seek to the correct location. Thanks to Ben for providing the test case!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3703 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 16:37:02 +00:00
43ca595d15
VCF headers now can be set to a particular VCF version after creation, which converts the header lines to the appropriate encoding on output. Plus some clean-up of the code.
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Also commented out the Tribble index out-of-date tests, the timing seems to be troublesome from the farm.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3702 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 05:32:14 +00:00
4995950d04
IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3701 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 04:40:31 +00:00
c9d5345150
Redo StratifiedAlignmentContext to use ReadBackedPileup's stratification options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3699 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 02:46:05 +00:00
dc4715c9c6
Permit empty fields in INFO and FORMAT structures - not fully tested yet but at least failing cases before now pass. Also, corrected a bug where in case we were reading 3.3 VCF's, or VCFs with no original allele encodings, we'd always print 2 bases per allele.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3698 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 01:56:07 +00:00
5f2b2d860e
Final stage of renaming
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3696 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 21:39:07 +00:00
6e7927a47d
Continuing the renaming nightmare...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3695 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 20:25:01 +00:00
9d7d5f1747
Continuing the renaming nightmare...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3694 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 20:24:27 +00:00
aa20c52b88
deleting vcf
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3693 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 20:19:15 +00:00
4195fc5c4e
renaming part 2...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3692 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 20:18:11 +00:00
6c9da5525d
renaming starting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3691 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 20:16:51 +00:00
b8d6a95e7a
Preliminary commit of new VCFCombine, soon to be called CombineVariants (next commit) that support merging any number of VCF files via a general VC merge routine that support prioritization and merging of samples! It's now possible to merge the pilot1/2/3 call sets into a single (monster) VCF taking genotypes from pilot2, then pilot3, then pilot1 as needed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3690 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 20:13:03 +00:00
178cf64a0c
Refactored ArgumentDefinition to absorb functionality from ArgumentDefinition and ArgumentTypeDescriptor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3688 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 18:37:58 +00:00
569456850d
Mark pointed out there's differentiation in the filter field. Rolling back.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3687 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 17:05:53 +00:00
52a474b27d
Fixed an issue with VCF combine in sites like the following:
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Broad: Filtered BC: No call
These were being treated the same as
Broad: Call BC: No call
Added some verbosity to separate them.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3686 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 16:49:31 +00:00
944dbb94ce
Refactored and generalized the database/comp annotations in VariantAnnotator. Now one can provide comp tracks as with VariantEval (e.g. compHapMap, comp1KG_CEU) and the INFO field will be annotated with the track name (without the 'comp') if the variant record overlaps a comp site (e.g. ...;1KG_CEU;...). This means that you can now pass 1kg calls to the Unified Genotyper and automatically have records annotated with their presence in 1kg.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3684 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 16:37:31 +00:00
47c4a70ac1
It turns out that it is legitimately possible for there to be reads that won't overlap within a target interval for cleaning. While we don't want to attempt cleaning, we also don't want to fail.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3682 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 15:50:44 +00:00
ae33d8a2f2
I just wanted one more vote. It's settled: we die.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3681 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 14:00:56 +00:00
8fb37f5f7a
For Kiran: warn the user when the actual and vcf ref bases differ so that if an exception is generated later, he knows why. All: should we generate the actual exception here? Is there any reason to allow cases where the vcf record has a different ref base than the actual reference? I'd vote that we die here. Thoughts?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3680 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 13:56:16 +00:00
d932322190
More necessary fixes for VCF4.0 - now results look more sensible in realistic, bigger VCF files produced by say Dindel and not just the small test VCF:
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- Fixed and cleaned code to produce trailing and padding bases in alleles around indels.
- Deal better with missing fields.
Pending:
- Chopping missing fields at end of genotypes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3679 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 02:59:30 +00:00
12c0de6170
Added ability to clean using only known indels. Added integration test for it. Fixed vcf->vc conversion for indels which was busted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3678 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 01:20:56 +00:00
610cc7ae2b
Cool package trick Kiran showed me. VariantEvaluator no longer public, AAT specifies the core package even though it lives in oneoffs. Disabled so integration tests pass.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3677 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 22:42:04 +00:00
4c6f4e41c6
Include making VariantEvaluator public within the package so my oneoffs can be seen (not included in previous submit specifically because I didn't want to break the build by changing anything in core...the road to hell is paved with good intentions)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3676 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 22:26:52 +00:00
9ac13b8f5d
Name and body change for this module to reflect local code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3675 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 21:45:26 +00:00
844cb2ed33
fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric!
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Also putting more tolerance into the timing on the tibble index tests (that check to make sure we're deleting out of date indexes, and not deleting perfectly good indexes). It seems that some of the farm nodes aren't great with a stopwatch.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3674 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 21:38:55 +00:00
101c27294d
Comment this guy out so we build again. (Hate it when my repository goes all funky.)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3673 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 21:16:33 +00:00
3017f82550
Initial commit of items for analyzing amino acid transitions in variant eval. Blew up my subversion by coding locally while i did not have internet. I hope this doesn't bust any integrationtests since I changed no existing code but...who knows. Crossing my fingers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3672 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 20:57:18 +00:00
e3fb4d5c70
Intermediate checkin, just to fix null pointer exception that happened when merging implementation with latest VCF4 decoder - field ORIGINAL_ALLELE_LIST in vc shouldn't be written in infoFields structure since this won't be output to file and there is no legal structure under this key.
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Base encoding for complex events is still brittle and most probably still has issues, fixes upcoming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3671 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 20:57:09 +00:00
baf9479c35
An addition for Sendu since he can't seem to tell when his CountCovariate jobs die in the middle of writing the CSVs. We now write an EOF marker at the end of the covariates table and look for it when reading in the file in TableRecalibrationWalker. By default, we warn the user if the EOF marker isn't present, but we exception out if the user provides the --fail_with_no_eof_marker option.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3670 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 18:50:07 +00:00
3ca2b7374b
Fixes to better deal with the "Type" and "Number" field in the INFO and FORMAT header lines in VCF4.0. We now record these fields and provide appropriate conversions. This is the first version that passes fully the VCF validator.
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Also, moved the flag indicating VCF4.0 to the VCFWriter constructor.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3669 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 16:43:00 +00:00
801b47c6e9
For Sendu: a similar addition to the Indel Genotyper allowing it to emit a metrics file (which for now consists only of # of normal/tumor calls made)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3668 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 13:19:17 +00:00
ddf87e61c2
For Sendu: optionally emit a metrics file with callability info (including number of actual calls made) from UG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3667 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 12:57:28 +00:00
929e5b9276
Fix possible null pointer exception
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3666 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 09:01:18 +00:00
2953c9f069
Efficiency improvement requested by the Picard team in IndexedFastaSequenceFile: improve the memory efficiency
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(and loading time) of long reference sequences by better controlling the input buffer size.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3665 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 07:22:07 +00:00
ed71e53dd4
1) Initial complete version of VCF4 writer. There are still issues (see below) but at least this version is fully functional. It incorporates getting rid of intermediate VCFRecord so we now operate from VariantContext objects directly to VCF 4.0 output.
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See VCF4WriterTestWalker for usage example: it just amounts to adding
vcfWriter.add(vc,ref.getBases()) in walker.
add() method in VCFWriter is polymorphic and can also take a VCFRecord, lthough eventually this should be obsolete.
addRecord is still supported so all backward compatibility is maintained.
Resulting VCF4.0 are still not perfect, so additional changes are in progress. Specifically:
a) INFO codes of length 0 (e.g. HM, DB) are not emitted correctly (they should emit just "HM" but now they emit "HM=1").
b) Genotype values that are specified as Integer in header are ignored in type and are printed out as Doubles.
Both issues should be corrected with better header parsing.
2) Check in ability of Beagle to mask an additional percentage of genotype likelihoods (0 by default), for testing purposes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3664 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 23:54:38 +00:00
4a451949ba
add parallel option to target creator for masking out reads with bad mates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3663 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 22:13:25 +00:00
6a23edd911
Fix performance tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3662 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 21:51:48 +00:00
20f5fdbcf7
Changes to MVC to make the the header of its output VCF compliant with spec (give expected # of values for info field annotations)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3660 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 18:33:23 +00:00
62d22ff1aa
adding the original allele list to a variant context (as the annotation ORIGINAL_ALLELE_LIST), in the case where the set alleles are the result of clipping. Added tests for both cases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3658 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 17:23:46 +00:00
1292c96e29
The cleaner now adds the OC (original cigar) and OS (original alignment start) tags as appropriate to reads that get realigned; this feature can be turned off. Also, improved integration tests (sorry, Kiran!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3657 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 16:46:47 +00:00
cc8d8eaedb
Now that we always reserve space for two read ends when collecting stats stratified by libraries, we need to check that the second end was indeed present; otherwise the pointer is null and this was causing an exception
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3656 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 16:40:16 +00:00
9a24598a98
By default, don't clean reads with mates mapped to other chromosomes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3654 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 15:14:20 +00:00
bf5cbad04c
Make the target creator a rod walker (that allows reads) so that we can easily trigger the cleaner on only known indel sites. Adding an integration test to cover this case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3651 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 13:28:37 +00:00
464ac63a22
Allowing N's in ALT field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3650 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 11:41:32 +00:00
3a9d426ca8
Added hasPileupBeenDownsampled() boolean to ReadBackedPileup, so that a pileup can report whether or not (but not how much) it's been downsampled.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3649 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 04:56:33 +00:00
8e848ccd84
SAMFileWriters can now write to /dev/null without throwing exceptions, so we can remove the try/catch blocks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3648 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-27 03:59:10 +00:00
09ccdf83b2
fixing a broken test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3647 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 21:59:00 +00:00
d6cbe4d0ad
Bug fixes to support haploid genotypes, optimization for indexing, now tracks the line of the VCF and catches errors to tell you the line no and line when a parsing error occurred.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3646 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 21:08:41 +00:00
5f8a3f95ef
The GT field once again reigns supreme (it must be the first genotype field). Thanks for the catch Eric.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3645 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 21:03:05 +00:00
75c98c42b8
Started path of deprecation of Sting's @Argument by splitting the annotation into @Output and @Input. Anything that's not an @Output should be an @Input.
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Checked in example qscripts that are basically todo integration tests.
Replaced use of queue @Input/@Output with Sting's new @Input/@Output. This means you'll now have to doc-ument the annotations.
More work on dependency resolution cycles being created in the graph during scatter/gather.
Filtering nulls to avoid NPE exceptions in scala's 'Collection'.hashCode.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3643 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 20:51:13 +00:00
147ba68441
Fixed bug with mrnaCoord field - made it count exon positions only, rather than introns & exons
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3642 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 19:53:32 +00:00
d3848745ab
moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3639 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 18:20:06 +00:00
b3edb7dc08
two fixes for the VCF 4 parser:
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- Allow the "GT" field in genotypes at any point in the genotype string (before we required they be the first key-value pair).
- Fix a bug with the phasing value put into the VariantContext, thanks for the catch Guillermo!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3638 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 18:01:23 +00:00
e15fe6858e
Disabling test - Will need to update big-tables soon.. will re-enable after updating md5
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3637 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 15:43:41 +00:00
f9c7803d4e
this got left off my last commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3635 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 02:42:44 +00:00
682f9b46c6
Two fixes together:
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1) Some improvements to the VCF4 parsing, including disabling validation.
2) Reimplemented RefSeq in the new Tribble-style rod system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3630 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 22:17:03 +00:00
62bc7651a8
fix for PSPW with DbSNP mask. Added an integration test for this case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3628 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 19:31:32 +00:00
8a9b2f4256
removing the GLF ROD.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3624 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 22:51:45 +00:00
611d834092
a couple of VCF 4 improvements:
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-Validation of INFO and FORMAT fields.
-Conversion to the the correct type for info fields (i.e. allele frequency is now stored as a float instead of a string).
-Checks for CNV style alternate allele encodings( i.e. <INS:ME:L1>), right now we exception out. Maybe we should just warn the user?
-Tests for the multiple-base polymorphism allele case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3622 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 20:21:43 +00:00
f0fc34bb8e
Bug fix: N's are allowed in the ref so don't fail when e.g. dbsnp has an N!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3620 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 17:49:14 +00:00
b6bceb39b0
Fixing up output for performance tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3619 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 17:00:17 +00:00
75d4736600
Committing changes to comp overlap for indels. Passes all integration tests; minor changes to MVC walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3618 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 15:49:13 +00:00
9b8775180e
Turn on the memory improvement by default (assume the target interval list is sorted, since it is 99.9% of the time). Make the user throw a flag when it's specfically not sorted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3617 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 15:44:55 +00:00
003dd4de3e
Rev Picard with performance enhancements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3615 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 22:54:23 +00:00
0cafd3d642
clip VCF alleles for indels: only a single left base, and as many right bases as align before converting to variant context.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3614 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 22:42:38 +00:00
9872b65803
clip to the null allele on the reference string in VCF 4, instead of stopping to perserve one reference base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3613 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 20:52:19 +00:00
b5df2705c9
-Remove Nway output option
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-Remove in-memory sorting
-Default to name-sorting (although we allow coordinate sorting with the --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe flag).
Cleaner, faster code. Wiki has been updated (including how to use FixMateInformation.jar from Picard). More changes coming soon.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3612 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 20:31:55 +00:00
30cf78fdc0
Refactoring for a first version of scatter gather api with basic shell script implementations.
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Modified build script so that queue is cleaned during "ant clean".
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3611 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 18:39:20 +00:00
a6d3e4bd47
Add code to allow reference alleles with 'N' in VariantContext, but not in the alternate allele(s). Also more updates to the VCF 4 code (fixed parsing for files without genotypes).
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This check-in will temperarly break the build (I need to see if Bamboo is correctly returning the log file for the failed builds).
Will be fixed once Bamboo starts building.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3609 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 18:26:37 +00:00
824c2bbac0
Finishing previous checkin
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3608 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 17:21:38 +00:00
4727bcda24
Removing Beagle output from UG. Use ProduceBeagleInput walker instead (since it can be run post-filtration and respects the FILTER column).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3607 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 16:56:37 +00:00
32f324a009
incremental changes to the VCF4 codec, including allele clipping down to the minimum reference allele; adding unit testing for certain aspects of the parsing. Not ready for prime-time yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3604 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 06:31:05 +00:00
de9f1f575f
Fixing command line parsing to accept negative number arguments. Command line definitions must now start with a letter or underscore; previously, they could start with a digit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3603 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-21 21:54:31 +00:00
9d6a341d15
Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose.
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Note: the -L argument takes both interval strings and filenames. If you specify an interval string that is also a file, an error will be thrown to move the file: ie. if you have a file "chr1" in the parent directory, GATK will ask you to move/delete it. But, this only happens with interval string arguments, NOT with intervals that are contained in files, which is a majority of the use case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3602 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-21 21:49:41 +00:00
300a18b85f
Updating the way reference data is processed, so GATK creates the .fasta.fai and .dict files automatically. If either (or both) don't exist, GATK will create them in the same folder as the fasta file. If it can't write the file, GATK will fail with a message to create them manually.
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Note that this functionality will only work if the directory with the fasta is writeable. GATK will fail if directory is read only and and either the .fasta.fai or .dict files don't exist. In the future, we could have these references be created in memory, but we decided against it this time.
Locking was also added to ReferenceDataSource so no issues come up while running multiple GATKs on the same reference: we don't want one process to be half-finished and another try to read it. So, you could see error messages related to locking. See ReferenceDataSource.java for explanation of the locking strategy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3601 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-21 21:42:42 +00:00
df1cadc4c9
Fix NullPointerException when priority list is left out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3600 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-21 13:46:54 +00:00
c806ffba5f
Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations
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will not be as fast as they could be because the workflow is currently merge sam records (sharding)
-> split sam records (LocusIteratorByState) -> merge records (LocusIteraotorByState) -> split
records (StratifiedAlignmentContext), but this will be fixed when StratifiedAlignmentContext
is updated to take advantage of the new functionality in ReadBackedPileup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3599 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-21 02:11:42 +00:00
1d50fc7087
Misc bug fixes: fix tracking of nInsertions with sample-split pileup constructor. Fix performance
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issue building up pileups from pileups of individual sample data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3598 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-20 20:32:27 +00:00
f18ac069e2
A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.
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Provides a cleaner interface with extended events inheriting all of the basic RBP
functionality. Implementation is still slightly messy, but should allow users to
provide separate implementations of methods for sample split pileups and unsplit
pileups for efficiency's sake.
Methods not covered by unit/integration tests have not been sufficiently tested yet.
Unit tests will follow this week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3597 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-20 04:42:26 +00:00
57a13805da
GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3596 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-19 21:36:41 +00:00
8ff93f77e6
Added evaluation module to count functional classes (missense, nonsense, etc.). At the moment, it only understands Cancer's MAF annotations. Added integration test for the functional class counting. Added better description for VariantEval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3595 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 21:51:40 +00:00
1e06d2bf68
Initial HLA Caller integration tests. Kind of painful, but will improve with code refactoring.
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This baby is now officially ours.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3593 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 20:35:27 +00:00
f44d8b150f
Mendelian Violation Classifier now filters violations on the fly via command line arguments; and closes unterminated homozygous regions at the end of a chromosome (so we see arms falling off in the file, rather than in the log)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3592 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 19:32:24 +00:00
aa1852575e
Add -noVerbose flag to stop output of INFO data.
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Cuts runtime by 30% and output from 65Mb to 1Kb.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3591 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 18:53:35 +00:00
724affc3cc
Major bug fixes for the Variant Recalibrator. Covariance matrix values are now allowed to be negative. When probabilities are multiplied together the calculation is done in log space, normalized, then converted back to real valued probabilities. Clustering weights have been changed to only use HapMap and by-1000genomes sites. The -nI argument was removed and now clustering simply runs until convergence. Test cases seem to work best when using just two annotations (QD and SB). More changes are in the works and are being evaluated. Misc fixes to walkers that use RScript due to CentOS changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3590 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 17:37:11 +00:00
c3434493b0
fixed integration test for VCF Header changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3589 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 16:31:48 +00:00
52477bd9e6
Add some missing methods to the pileup architecture.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3588 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 15:03:08 +00:00
5050b19457
We're unable to make the naive deduper more worldly, so we're killing it instead.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3587 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 13:54:27 +00:00
42e7ff4f28
forgot to update a test, the md5sum of the underlying file changed (which is recorded in the ROD tests).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3586 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 13:27:56 +00:00
b978d5946b
adding changes for VCF 4, mostly in the way we handle VCF headers. The header fields are now aware of the differences between different VCF formats. There was also a bunch of clean-up of out-of-spec VCF used in the tests (mismatched VCF file format fields, etc), and updates to the associated integration tests. Also some logging statements for BTI.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3584 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 08:23:23 +00:00
e26a273ef5
Turned the test back on
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3582 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 22:57:42 +00:00
48cbc5ce37
Merging the sharding-specific inherited classes down into the base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3581 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 22:36:13 +00:00
612c3fdd9d
First pass at eliminating the old sharding system. Classes required for the original sharding system
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are gone where I could identify them, but hierarchies that split to support two sharding systems have
not yet been taken apart.
@Eric: ~4k lines.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3580 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 20:17:31 +00:00
b694ca9633
Cleanup: Don't require likelihood ROD in Beagle parameters when generating output VCF. Likelihoods file is only an input to Beagle but the Walker that generates a VCF doesn't need it, so it's silly to ask for it and it's error-prone.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3579 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 17:45:48 +00:00
c1595a383a
More bugfixes for cases where no sample name is present.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3578 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 16:46:02 +00:00
3d049204ed
some refactoring for the variant eval output system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3576 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 05:34:31 +00:00
db1383d0b2
Rev the latest version of Picard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3575 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 23:55:07 +00:00
5b370ffc62
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3574 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 20:42:58 +00:00
5972ad1199
Fixes to mrl integration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3573 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 20:40:10 +00:00
b75ded61b8
Removing obsolete rod; no longer needed given previous addition to SampleUtils.
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JIRA GSA-318
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3572 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 20:03:14 +00:00
c671864228
Re-allowing blacklist by read group id.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3571 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 19:45:44 +00:00
f003703912
Allow specification of particular rods for pulling out sample names.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3570 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 19:37:09 +00:00
01ffa307c2
When going NWay out in the cleaner, use the new *merged* header (instead of the original one) for each bam file so that it matches the new uniquified read group ids in the reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3569 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 19:36:36 +00:00
05c2f96bb4
Small update to the command line docs for read_group_black_list.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3568 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 19:23:34 +00:00
d7f3102c3f
Fixed read group blacklist filter to look only at readgroups (and not the read's themselves). Otherwise, it fails when attribute tags with different meanings show up in both places (e.g. SM). Added performance improvement.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3567 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 19:14:37 +00:00
e77f76f8e1
Reenabled downsampling by sample after basic sanity testing and fixes of the
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new implementation. Hard testing and performance enhancements are still
pending.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3566 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 17:23:27 +00:00
c44fd05aa1
Fix for a reflection issue with generic types.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3565 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 15:58:38 +00:00
7a91dbd490
Renamed some of the column names in Ti/Tv and Concordance modules so that they are clearer. Removed ValidationRate module (it was busted).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3564 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 15:53:06 +00:00
8cb16a1d45
a) Cleanup, remove -input argument from BeagleOutputToVCFWalker since it's not needed.
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b) Added back old Beagle ROD to maintain backward compatibility (does anyone even use this???)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3563 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 02:13:08 +00:00
d319a28be7
Complete rewrite of the Beagle functionality to read from Beagle output files and produce VCF with modified genotypes. Now, a new ROD system using Tribble is in place. Beagle inputs are set using -B beagleType,Beagle,pathToBeagleFile, where beagleType can be either beagleR2, beagleLike, beaglePhased or beagleR2 (BeagleOutputToVCFWalker requires all of the above). Only pending items: -input argument is now unused and can be removed, will be cleaned later. Wiki will be updated with new usage shortly.
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We can now run with a reduced memory footprint, and output VCF is exactly identical to previous version. Drawback is increased runtime because Tribble has to create an index for all the Beagle files when starting if the idx files are missing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3562 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 02:01:35 +00:00
d265397bf6
removing a reference to a unused internal Sun class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3560 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 15:27:57 +00:00
42b8a8f295
slight change in output format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3559 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 14:52:04 +00:00
32fc221ffe
Replaced pattern matched pipeline spec with annotated objects.
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Old version is no longer available.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3558 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 04:43:46 +00:00
b99a5e06f3
Added option to only consider alleles of > specific allele frequency.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3557 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 02:09:35 +00:00
8a895f481f
Proper exception chaining for troubleshooting Sendu's issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3556 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 01:38:36 +00:00
8defb30796
Documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3555 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 21:31:01 +00:00
c1046653a2
Fixed handling of records where gene-names are identical (eg. as in refseq NR_030638 in chr20)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3554 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 20:00:49 +00:00
1e42984a16
Improved buffer-size arg handling
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3553 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 19:59:15 +00:00
b3c3023c3c
Allows callers to handle HLA reference files as input (rather than hard-coded paths)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3552 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 18:56:08 +00:00
9666d47d17
ooops, debug print now removed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3550 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 18:07:12 +00:00
abdc8521ea
Added debug options for FindClosestHLAWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3549 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 17:52:03 +00:00
c38390eabb
Added option for min number of matches between reads and alleles required to consider reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3548 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 16:08:49 +00:00
4ab1f440c3
A new argument: --targetIntervalsSorted (boolean flag). If specified, the interval file is assumed to be sorted (duh!) and it is NOT slurped into the memory but instead traversed directly on disk as needed. If the file turns out to be unsorted, an exception will be thrown at the point where inconsistency occurs (can be late into the processing!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3547 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 16:00:22 +00:00
671ac00748
A simple utility class that implements a merging Iterator<GenomeLoc> built over an interval or bed file (this is NOT a rod, but rather a direct line-by-line file reader that converts strings to genome locs on the fly and merges overlapping intervals)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3546 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:54:37 +00:00
f137bf8f85
now adaptor silently skips empty lines in the underlying string iterator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3545 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:35:07 +00:00
d8c963c91c
Remove PhaselikelihoodsWalker.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3544 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:21:43 +00:00
5704294f9d
HLA caller updated - now searches all (common and rare) alleles, more efficient read filtering and allele comparison runs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3543 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:14:40 +00:00
d51e6c45a7
a utility class; turns string iterator into GenomeLoc iterator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3542 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 14:07:44 +00:00
7b7d3341f0
trivial refactoring: isFile renamed to isIntervalFile and made public
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3541 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 14:02:23 +00:00
c3b68cc58d
Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept
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independent while processing, and only merged back in a priority queue if necessary in a special
variant of the ReadBackedPileup. This code is not live yet except in the case of naive deduping.
Downsampling by sample temporarily disabled, and the ReadBackedPileup variant is sketchy and
not well integrated with StratifiedAlignmentContext or the walkers. Cleanup to follow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3540 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-13 01:47:02 +00:00
804facb0cc
Removing these utilities as part of a hostage negotation with Matt. Can I have my journal club paper now?!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3539 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 21:41:29 +00:00
e6d8faf293
making 'parseLocation' public static - as simple as the logic is, it's better kept in one place and I need it!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3537 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 18:19:59 +00:00
8c28be5933
Fixing a VCF bug for Sendu: we weren't emitting flags (booleans) correctly in VCF3.3 (rev'ed tribble for this).
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Updated dbsnp/hapmap membership info fields to be flags now instead of ints.
While I was there, I added the change in the Annotator for Jan to force reads to be from a specific sample.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3536 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 16:42:06 +00:00
22620ba95c
Adding "abi_solid" to the list of known platforms.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3534 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 13:37:19 +00:00
63ad71cca6
Fix busted code. Note for all:
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String.valueOf(byte[]) doesn't work. You must use new String(byte[]).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3533 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 05:01:48 +00:00
338bb9adf4
CommandLineProgram for measuring java I/O speeds for large plain-text or gzipped files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3532 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 21:34:37 +00:00
06fc5eecf8
Implemented TreeReducible - if num threads > 1, the output will be accumulated in memory and written to a vcf file at the end - in onTraveralDone(..). If num threads == 1, things will work as before - where vcf records are written to disk as soon as they are computed with map(..).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3530 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:57:23 +00:00
3b375cb237
Sped up parseGenomeLoc(..) by replacing regexp with String.indexOf(..) - attempt 2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3529 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:54:36 +00:00
99b684ea89
Adding new support for reference data. ReferenceDataSource is a new class that manages reference data, and allows IndexedFastaSequenceFile to be a simple reader. This checkin also includes FastaSequenceIndexBuilder, which reads a fasta file and creates an index, like samtools faidx. Right now this is not enabled, because we are still working out thread safety. So the only new UI change is that GATK can be run without a fai file. Soon, we will enable 1) GATK to be run without a dict file too, and 2) both dict and fai files will be saved on disk for future program executions. For more info, see ReferenceDataSource.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3527 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:10:23 +00:00
f55f32d4ee
Bug fix.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3526 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 01:53:26 +00:00
ca4eab1d23
Now annotations that require reads return null if there's no alignment context, so that running without reads adds annotations only for the appropriate fields.
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Added an integration test for the read-less case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3525 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 20:36:46 +00:00
6941c81bfa
reverting revision 3522 to the old code until we fix the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3524 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 19:25:02 +00:00
dbee21a50f
Bugfixes for the case when no read groups / no samples are available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3523 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 18:47:05 +00:00
adc4c4e577
Sped up parseGenomeLoc(..) by replacing regexp with String.indexOf(..)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3522 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 18:11:43 +00:00
20167fd411
Final changes to MVC -- associates variants with regions of homozygosity in child and parents, corrects for genotype errors, and prints out a separate file with informationf or each region of homozygosity.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3521 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 18:05:37 +00:00
fdded73861
Improved error reporting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3520 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:52:48 +00:00
4f00e265a8
quick update for a change I implemented for Ryan
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3519 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:23:31 +00:00
ad98512f6c
adding changes so that we look at the headers already loaded by the engine for samples and other VCF utils, and not create readers for each file to get them (this caused Tribble to regerenate indices if the index file can't be written to disk).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3518 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:21:12 +00:00
c1b7bcc786
Fixed handling of mitochondrial genes - added special cases such as ATT being a start codon in mitochondria. Added warning if a gene doesn't start with Met or end in a stop codon
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3517 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:15:47 +00:00
4f1181974b
Added toString() method
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3516 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:12:57 +00:00
9b2fcc4711
Refactoring of the annotation system:
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1. VA is now a ROD walker so it no longer requires reads (needs a little more testing)
2. Annotations can now represent multiple INFO fields (i.e. sets of key/value pairs)
3. The chromosome count annotations have been pulled out of UG and the VCF writer code and into VA where they belong. Fixed the headers too.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3513 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:05:51 +00:00
84563b37e5
Partial flattening of the hanger data structure. Hanger data structure is
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not currently as flat as it could / should be, but it's already comparable
to the speed of the reference implementation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3512 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 16:28:49 +00:00
8f9e3e8ad7
Commit for Kiran; but this is now working, barring little exceptions that I've yet to run across...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3511 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 14:21:19 +00:00
6d5556939d
updating Tribble with a couple of important Tabix fixes, and updating the variant eval integration tests to run each test with both plain vcf and gzipped tabix (added the tabix version
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to the vlidation directory), using the same md5sum.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3509 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 01:47:04 +00:00
c2858c8988
Minor performance enhancement. Checkpoint commit before major performance
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overhaul.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3504 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 21:39:39 +00:00
5ed2818ffb
Forgot to commit code i relied upon
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3503 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 21:01:35 +00:00
736098b58d
A quick commit before running home. This is a re-factored version of the OppositeHomozygoteClassifier which will work with deNovo violations as well. Some code still needs to be migrated from OHC which is wy that walker isn't yet deleted. This'll be up and running tonight.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3502 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 20:47:01 +00:00
de134c226d
Removed ability of users to specify annotations to recompute, cleanups.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3501 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 19:17:59 +00:00
4d1a6b3d99
quick changes for G
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3500 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 16:33:27 +00:00
907931c902
a) Update annotations when creating new vcf with Beagle's imputed data. Since genotypes may (will) change based on imputation, several annotations need to be updated. By default, AC, AF, AN and AB will be updated. User can force extra annotaqtions to be updated with -A <annotation> argument.
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b) Several cleanups and beautifications.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3499 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 15:12:04 +00:00
933133ee28
Initial commit of the opposite homozygote classifier. Currently does the following, given a trio vcf:
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+ Identifies opposite homozygote sites
+ Identifies the parent from whom it is expected that a null allele was inherited (or whether it was a putative genotype error; e.g. mom=homref, dad=homref, child=homvar)
+ Labels each opposite homozygote with its homozygous region in the child (e.g. region 1, region 2)
+ Labels each opposite homozygote with the size of the homozygous region in which it was found, the number of child homozygotes in the region, and the number of opposite homozygote violations within that region
To come:
+ Classification of sites as likely tri-allelic
Note that this is very experimental
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3498 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 03:56:07 +00:00
199e4208cd
Bug fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3497 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 00:30:33 +00:00
52ab9f2417
Feature parity between LocusIteratorByState, DownsamplingLocusIteratorByState, including pushing mrl /
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the LocusOverflowTracker into LocusIteratorByState. Note that the 'Matt Hanna exception', is still enabled
because I haven't yet validated the performance of the DownsamplingLocusIteratorByState when running
without downsampling.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3496 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-07 22:58:21 +00:00
5c4d070566
Push Mark's changes in LocusIteratorByState into DownsamplingLocusIteratorByState
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in preparation for merging the two into one.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3495 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-07 17:29:30 +00:00
6eeb1693ca
JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3494 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-07 00:33:02 +00:00
c1ecf75dd5
Update to the latest rev of the picard sharding patch. Includes updates reflecting
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the imminent move of IlluminaUtil into picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3493 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-06 20:33:21 +00:00
c503f01dcf
More cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3492 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-06 17:41:38 +00:00
d4c66d6191
a) Small cleanup
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b) Fix major issue with Beagle likelihood converter: if likelihood triplets from UG end up being too low, then Beagle input file will be produced with 0.00,0.00,0.00 triplet. If all samples at a marker have this issue, Beagle will effectively produce junk. To fix, likelihoods are renormalized before converting to linear space.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3491 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-06 17:31:59 +00:00
cfa18f6743
Fixing missed update with new Allele in it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3490 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 23:56:34 +00:00
3ea506fe52
No more new Allele() -- must use create. Allelel simple alleles are now cached for efficiency reasons. VCF4 codec optimizations -- 4x performance in general. Now working in general but hooked up to the ROD system now as VCF4. WARNING -- does not actually work with indels, genotype filters, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3489 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 23:03:55 +00:00
ef47a69c50
a) First fully functional (sort of) version of walker that parses Beagle imputation output files and produce a vcf with imputed genotypes.
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More doc/info to follow shortly. Issues still to be solved:
a) Walker changes all genotypes based on Beagle data, but annotations on the original VCF are unchanged. They should in theory be recomputed based on new genotypes.
b) Current implementation is ugly, dirty unwieldy and will necessitate a refactoring soon so I can keep my pride. Most aesthetically affronting issue right now is that we read the full Beagle files at initialization and keep them in memory, but a more delicate implementation would just read from files on a marker by marker basis. Issue that currently prevents this is that BufferedReader() instances don't seem to play nice when called from the map() function.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3488 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 20:37:25 +00:00
b811e61ae1
Optimized, nearly complete VCF4 reader 2-4x faster than the previous implementation, along with a VCF4 reader performance testing walker that can read 3/4 files, useful for benchmarking
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3487 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 18:11:38 +00:00
6482b87741
adding the super experimental, half-broken, generally crippled, awkwardly commented, header ignoring vcf4 code. Don't use this, unless you're a developer for VCF4. If so, remove the exception from the constructor so that it won't always exception out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3486 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 07:38:46 +00:00
0b03e28b60
updating the tribble library to include the reference dictionary reading / writing. We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this). Also renamed some classes to be more reflective of their function.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3485 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 06:34:26 +00:00
3d055e3d16
Fail fast if users try to parallelize a read walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3484 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-03 18:14:33 +00:00
7d79848f40
Better error message when bam file / list file with wrong extension is
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supplied.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3483 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-03 17:52:48 +00:00
597b3744ab
Always use phasing info when converting genotypes to strings
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3482 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-03 17:50:50 +00:00
e2b41082af
GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3481 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 22:26:32 +00:00
8ec091d6d2
re-enabling regeneration of the tribble index if it's out of date. Also moved the class that can detect text in the log4j stream (useful in testing to make sure appropriate messages are generated).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3480 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 17:45:51 +00:00
f0c379dde8
Unconsequential changes in report formatting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3479 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 17:43:25 +00:00
3ab936181c
Supports the join feature of GenomicAnnotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3478 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:29:57 +00:00
f5f7217413
Implemented joins
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3477 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:28:53 +00:00
09c3b15af3
Implemented joins
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3476 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:28:06 +00:00
e14ae471a0
Refactored some of the small utility methods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3475 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:26:00 +00:00
898a78e97d
Added toString()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3474 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:24:25 +00:00
12c3e3ecda
Added back the check for values.size() != header.size(). Now exception will be thrown if number of columns in a record doesn't equal number of columns in the header
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3473 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:23:05 +00:00
290771a8c2
Automatic cutting of recalibrated variant calls using ApplyVariantCuts. VariantRecalibrator produces the tranches plot alongside the optimization curve. Specify the levels using -tranche 1.0 -tranche 5.0 etc
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3472 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 15:03:00 +00:00
4a555827aa
Removing more toUpperCase sanity checks
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3471 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 14:38:39 +00:00
56e504789a
trivial change: toUpperCase no longer necessary
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3470 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 14:00:47 +00:00
87fe60fe4f
Fix for Sendu. new Process and p.waitFor() don't seem to work on his farm. Throws an IOException. This was a problem way back with AnalyzeCovariates too.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3469 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 11:37:10 +00:00
7f0c638653
Fix for the indel cleaner: I forgot to "unclip" the cigar string (even though the clipped bases were removed) before using it as an alternate consensus in a particular instance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3468 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-01 02:07:20 +00:00
21427211c0
Personal MD5 database system now live. WalkerTest now maintains a database of result files associated with MD5 results in integrationtest/, and provides command lines for diff-ing expected to current md5 results when encountering failed intergration tests. The suite currently takes 200Mb to store. Update and run intergrationtest to build your very own expectation database for future development work.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3466 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-31 16:06:16 +00:00
2b02324587
Support for detecting and automatically excluding reads reading into the adaptor sequence and, if desired, also only showing the first pair when two reads overlap in the fragment. Not enabled, an intermediate check in before updating and verifying the impact on locus walkers everywhere.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3465 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-30 18:00:12 +00:00
eb25e41111
minor update to new tribble name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3462 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 20:23:25 +00:00
ffeb3fd80d
Thanks to Guillermo, I found a bug in the Unified Genotyper output: GL was posteriors instead of likelihoods. Not a huge deal because the
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priors were flat, but fixed nonetheless.
Also, needed to update Tribble.
Minor updates to the Beagle input maker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3461 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 19:28:26 +00:00
4e268ef6ac
Removing the Variant Recalibration Performance test because it isn't ready yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3460 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 18:27:25 +00:00
522dd7a5b2
Adding the variantrecalibration classes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3459 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 18:21:27 +00:00
2014837f8a
VariantOptimizer package is moved to core, renamed as VariantRecalibration, and added to the binary release package. VariantOptimizer walker is renamed to GenerateVariantClustersWalker and ApplyVariantClustersWalker renamed to VariantRecalibrator. Integration tests added, performance tests still to be done.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3458 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 18:20:18 +00:00
871cf0f4f6
Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:
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@Requires(value={},referenceMetaData=@RMD(name="eval",type= VCFCodec.class))
you'd say:
@Requires(value={},referenceMetaData=@RMD(name="eval",type= VCFRecord.class))
Which is more in-line with what was done before. All instances in the existing codebase should be switched over.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3457 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 14:52:44 +00:00
cc2bf549c8
Removing my unnecessary optimization. 10 lines later in the code the same optimization was applied. A monumental waste of time.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3455 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 14:10:48 +00:00
a4d834cc01
fixing the test I broke
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3454 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 02:06:20 +00:00
6485e8383d
Trivial change to retrigger broken build that really isn't broken
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3453 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 23:33:46 +00:00
f2e7582cfc
Reorganization of SW code for clarity. Totally failure at raw optimization. Discovered that ~50% of reads being cleaned were perfect reference matches. New code comes with flag to look at NM field and not clean perfect matches. Can we turned off with command line option (needed for 1KG bams with bad NM fields). Going to rerun cleaning jobs due to accidentally rebuilding of stable codebase and loss of 2 days of runtime.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3452 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 23:16:00 +00:00
e1b0aefb29
fix for parallelism bug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3451 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 22:16:14 +00:00
cded9ec985
adding a command line option, -etd (enable threaded debugging), that uses a custom thread pool class to catch exceptions thrown inside of a thread.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3450 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 21:57:56 +00:00
e2674671e7
The liftover code needs to *hard filter* records whose reference changes (since they no longer adhere to the VCF spec as they don't match the new reference - and can't be converted to VariantContext).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3448 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 19:22:47 +00:00
ff4a0764df
Read error rate is now parallelizable
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3447 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 19:00:09 +00:00
dfc36c1e95
Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3445 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 22:12:25 +00:00
3873dccb35
First fully functional (though preliminary) version of walker that takes an input VCF and outputs a Beagle .bgl file that can be used for missing genotype calls/haplotype imputation. For now, only supported input format is likelihood format for unrelated individuals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3444 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 21:03:23 +00:00
f9efc1248c
VariantEvalWalker now takes indels if you throw the -dels flag. IndelLengthHistogram appears to be working properly, it is turned off by default (as it is experimental) but you can turn it on in your own repository.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3443 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 20:03:14 +00:00
058441fa39
Trivial renaming of test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3441 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 16:56:42 +00:00
0265199ce4
First pass at an IndelLengthHistogram module for variant annotator. Off by default. Will be tested shortly (have to commit, so I can check out in another directory, so that compiling won't kill all my jobs running on LSF)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3440 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 15:04:39 +00:00
a2fab07258
fixed the build problem: there were two copies of the AnnotatorInputTable Codec and Feature in two different spots.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3439 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 14:47:15 +00:00
5928047d8b
Optimization of reference window calculation to us bytes not char and no uppercasing since reference and read bases are always uppercase now. Should remove some ~5% of runtime of UG.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3438 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 14:10:26 +00:00
88a06ad81f
Changes to Depth of Coverage:
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- For speedup in large number of samples, base counts are done on a per read group level, then
merged into counts on larger partitions (samples, libraries, etc)
+ passed all integration tests before next item
- Added additional summary item, a coverage threshold. Set by (possibly multiple) -ct flags,
the summary outputs will have columns for "%_bases_covered_to_X"; both per sample, and
per sample per interval summary files are effected (thus md5s changed for these)
NOTE:
This is the last revision that will include the per-gene summary files. Once DesignFileGenerator is sufficiently general, and has integration tests, it will be moved to core and the per-gene summary from Depth of Coverage will be retired.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3437 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 03:39:22 +00:00
0607f76a15
commenting out this test until I can figure out what the hell is going on with the codecs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3436 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 01:12:10 +00:00
062b316881
Better Exception message when can't find annotation value in variant recalibrator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3434 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-25 21:15:50 +00:00
bf530d23de
Variant Recalibrator now makes use of a prior on known/novel status as well as on allele frequency spectrum. The VariantOptimizer walker now clusters with all variants but gives more weight to knowns / hapmap / 1KG / MQ1 sites. The weights are all optional command line arguments. We no longer assign default values to annotations that are malformed. The walkers will crash with exception so as to not cover up potential issues. We only produce titv-less clusters now, and so the titv argument in VO was removed and the WithoutTiTv string that gets added to the cluster file is removed. The wiki is updated to show new example commands.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3433 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-25 21:08:31 +00:00
ae6c014884
Fixed UG parallelization bug. Better integration test to catch this in the future.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3432 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-25 21:03:45 +00:00
434e920da9
Oops, forgot to update integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3431 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-25 20:37:45 +00:00
772f558ae0
Massive change to the indel realigner code. We now properly deal with soft-clipped reads. Also, improved left-alignment code.
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Small change for Ryan to get hard-clipped reads working for the recalibrator.
PLEASE DO NOT RELEASE THIS WEEK. I still have some more testing to do and need Mark to run WG jobs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3430 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-25 20:04:33 +00:00
f3e2aae570
add experimental support for tabix files (for any of our Tribble rod types), as long as they end in .gz and can be read by the tabix reader.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3429 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-25 04:44:46 +00:00
8db7c97c4d
Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3427 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-24 14:38:54 +00:00
4aa749c709
Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3426 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-24 14:38:07 +00:00
aca3bcb193
Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3425 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-24 14:37:17 +00:00
64ed770250
Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3424 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-24 14:36:28 +00:00
ee3f2eb1d0
Don't output traversal reduce result in the logger. In many cases, the reduce
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result is tangential to the product of the analysis and having the logger always
emit it can confuse the output (such as in the new reduceByInterval
DepthOfCoverage walker). If users want to emit it, they can choose not override
onTraversalDone, or override onTraversalDone and write results to the output
stream / logger / whatever their choice.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3422 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-23 22:41:43 +00:00
a40e64e47b
A downsampling validator. Compares the generated pileup passed in from the alignment context to the reads,
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passed in as a Tribble SAM text feature. If the generated pileup contains a valid set of reads according to
the downsampling rules, the test passes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3421 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-23 21:49:54 +00:00
a280a0ff0d
a) Made HaplotypeScore default annotation. This changed several integration tests, whose MD5 is now updated.
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b) Disabled BaseQualRankSumTest, the returned p-values differ wildly from Matlab/R-provided ones, cause TBD.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3419 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 22:25:17 +00:00
b10950c691
Simple performance optimization -- cache the number of reads in the locus hanger.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3417 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 19:26:16 +00:00
355396109b
Bug fix to avoid build failure (class changed under me??)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3416 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 18:48:56 +00:00
1753d07b02
Added AnnotationByAlleleFrequencyWalker - walker takes an input vcf, a reference vcf and a list of annotations (with the -A argument). For each site present in both VCF's, it outputs the given annotations into the screen as well as allele frequency. Since HapMap vcf reference doesn't include AF in annotations, it computes it from Chromosome, Het and HomVar counts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3415 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 18:31:34 +00:00
745d7c582f
added integration test for intervals with no coverage due to filtering
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3414 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 16:52:42 +00:00
7fb3f2d3eb
Annotator now buffers indel calls (prevents double-output from double-calls to map)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3413 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 16:34:34 +00:00
4e834b5e35
VFW now uses a ref window and thus is compatible with indels.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3412 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 15:59:42 +00:00
88cb93cc3c
Changes to Depth of Coverage (added maximum base and mapping quality flags; with new integration tests -- because they use b36, and the other test uses hg18, it's in a different class (integration test system can't change refs on the fly). Initial change to VariantAnnotator to allow it to see extended event pilups; you currently have to throw the -dels flag; and it's specified as "very experimental". Yet,all the integration tests pass.
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Homopolymer Run now does the "right" thing (e.g. single bases are represented as HRun = 0 rather than HRun = 1) for indels. AlleleBalance now does something close enough to correct.
Added a convenience method to VariantContext that will return the indel length (or lengths if a site is not biallelic).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3409 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 13:02:01 +00:00
6faf101c6c
Minor improvements to Callable Loci for public consumption
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3408 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 12:50:11 +00:00
388dd8d64d
Fixing bugs in downsampler introduced when I added Ryan's dup eliminator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3407 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 02:53:12 +00:00
a10fca0d5c
Genotyper now is using bytes not chars. Passes all tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3406 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 21:02:44 +00:00
7389077b3b
A few misc usability fixes:
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- Clarify the message emitted when -XL is supplied so I don't spend another half day chasing a bug that doesn't exist.
- Crash with a helpful message when running -nt with non-TreeReducible walkers.
- Crash with a helpful message when running -nt with reduceByInterval walkers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3405 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 19:02:02 +00:00
b543dd4ac4
more aggressive checks for the locking, and some more documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3404 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 16:16:36 +00:00
1ab00e5895
Retiring multi-sample genotyper
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3401 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 14:10:56 +00:00
727822adb4
BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3400 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 14:05:13 +00:00
6ce3835622
Removing unused methods in QualityUtils; ReferenceContext now converting all bases to upper case, but can be disabled with static boolean
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3399 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 12:38:06 +00:00
5abac5c057
A few more char -> byte cleanups
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3398 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 00:02:06 +00:00
8a725b6c93
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3397 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 23:27:55 +00:00
02cc1afdc8
remove RodBed and all it's dependencies.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3396 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 19:12:30 +00:00
ffb1b46166
Added a GCCalculatorWalker for a oneoff analysis for Mark Daly (GC content of agilent 1.1 targets)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3395 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 18:49:51 +00:00
0036df7b03
adding a convenience method for getting at the RODs that overlap a specific locaiton as GATKFeatures.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3394 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 17:40:20 +00:00
ca386439be
only emit a warning if the tribble index is out of date, don't remove and replace it for them. Added a test case where the log4j appender checks the logging messages for the appropriate output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3393 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 15:12:48 +00:00
017ab6b690
Experimental versions of downsampler and Ryan's deduper are now available either
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as walker attributes or from the command-line. Not ready yet! Downsampling/deduping
works in a general sense, but this approach has not been completely optimized or validated.
Use with caution.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3392 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 05:40:05 +00:00
46ba88018d
Updated to the new readHeader(..) api
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3391 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 04:06:34 +00:00
984c51efd3
Updated to use Tribble-based GATKFeature instead of TabularROD
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3390 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:42:12 +00:00
42ee16f256
Updated to use Tribble-based GATKFeature instead of TabularROD
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3389 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:41:37 +00:00
d8469e2fba
Updated to use Tribble-based GATKFeature instead of TabularROD
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3388 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:40:47 +00:00
d65b2d32d1
Removed AnnotatorROD which has been ported to Tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3387 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:39:34 +00:00
b82116f488
Removed AnnotatorROD which has been ported to Tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3386 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:39:20 +00:00
6b96f025f5
Tribble integration for indexing the AnnotatorInputTable format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3385 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:37:54 +00:00
2f3933148d
Added fast split(str, delimiter) methodf
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3384 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:37:26 +00:00
aedb9f6734
Bring SAMPileupCodec into compliance with new interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3383 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 01:23:29 +00:00
7cfb9ff3dc
updates for Tribble 82, fixes for Ryans case where multiple processes would attempt to read/write to the same index, and a couple other Tribble-centric bug fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3382 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 19:34:45 +00:00
635f61c22d
Clone the other guy too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3381 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 18:56:01 +00:00
9e15299475
Misc cleanup in variant recalibrator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3380 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 17:37:01 +00:00
eb200e4cce
Hrumph. Don't just add pointers to the same objects, actually clone the underlying arrays.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3379 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 17:13:44 +00:00
e016491a3d
Major refactoring of Depth of Coverage to allow for more extensible partitions of data (now can do read group, sample, and library; in any combination; adding more is fairly easy). Changed the by-gene code to use clones of stats objects, rather than munging the interval DoCs. (Fix for Avinash. Who, hilariously, thinks my name is Carl.) Added sorting methods to ensure static ordering of header and body fields.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3377 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 16:58:13 +00:00
3c022e4b0c
Improved command-line-arg validation at startup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3374 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:46:17 +00:00
35b4bba35e
Refactored so it could be used for knownGene and CCDS as well as refGene
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3372 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:44:10 +00:00
bb86c0e03a
Improved error message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3371 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:43:13 +00:00
68719615be
For multiple matches, shifted counter to be 1-based
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3370 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:41:50 +00:00
73e2e32837
Fix typo.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3369 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:04:00 +00:00
ebd0fabf86
First pass updates to annotations to work with indels. HomopolymerRun indel behavior is currently turned off by a global boolean until it's ready to go live.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3368 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:02:13 +00:00
0791beab8f
Checking in downsampling iterator alongside LocusIteratorByState, and removing
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the reference implementation. Also implemented a heap size monitor that can
be used to programmatically report the current heap size.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3367 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:00:44 +00:00
b7d21627ab
Changes to DepthOfCoverage (JIRA items) and added back an integration test to cover it. Alterations to the design file generator to output all transcripts (rather than choosing one at random).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3366 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 17:23:00 +00:00
4235164359
Removed the confusionMatrix column (of *course* this is a confusion matrix... what else would it be?!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3365 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 21:55:37 +00:00
95b29f608b
Specify default values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3364 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 21:42:53 +00:00
6efd05831b
Encapsulating annotation decoding function in order to use same fixed random seed in both VariantOptimizer and ApplyVariantClusters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3363 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 20:03:38 +00:00
32389dc0a9
Fixed GQ estimate when chosen genotype isn't the most likely according to the GLs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3362 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 19:17:46 +00:00
1538dc0144
optimizer now uses -an arguments instead of exclude and force for clarity. command-line length reduced by 50%
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3361 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 15:41:44 +00:00
88bd7a2045
Reenabling UG parallelization performance tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3360 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 16:28:08 +00:00
0490909285
Fixed epic generic paths fail.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3359 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 15:59:57 +00:00
7ef87e5126
An integration test based on validating pileup to test parallelism in reads, reference, and RODs. This test runs in less
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than a minute and fell over instantly in the case of the Tribble parallelism issue.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3358 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 15:40:43 +00:00
ceec525420
Got rid of stray unicode characters in copyright message.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3357 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 14:47:39 +00:00
3e9ad4bbd0
Porting SAM pileup ROD to Tribble as a case study.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3356 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 00:22:59 +00:00
6839c194cb
although holding on to memories can be fun, it's bound to hurt performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3355 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 19:26:58 +00:00
c81b910f73
Commenting out the parallelization test which is failing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3354 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 18:39:53 +00:00
cac98ba5ef
a couple of small documentation fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3353 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 17:40:27 +00:00
3f07611187
Added support for -nSamples to varianteval (and getNSamplesForEval function). Allows you to calculate AC based metrics for files without genotypes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3350 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 13:36:31 +00:00
2c55ac1374
fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3349 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 06:13:26 +00:00
6868ce988f
Fix hanging bug reported by Susanne Pfeifer (tiffy @ get satisfaction) where, if the last read(s) in a shard all have an
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indel in roughly the same location and that indel isn't covered by any other reads, LocusIteratorByState goes into an infinite
loop.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3348 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 17:31:19 +00:00
34969f304c
Adding dbsnp to all UG performance tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3347 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 15:48:05 +00:00
140e43b93b
Checking in to see whether it fails. If I start getting bombarded with Bamboo error reports, I'm commenting it out...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3346 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 15:39:42 +00:00
572b383fe2
Make VA annotate dbsnp again
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3345 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 14:06:53 +00:00
b09e7231d1
A quick implementation of the experimental covariates for the TGen folks to work with.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3344 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 01:08:52 +00:00
aec5f7b630
Can now threshold results based on minimum base and/or mapping quality.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3343 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 19:58:07 +00:00
13fd182b7c
For dealing with slightly malformatted BAMs - mark every alignment as primary, or in the case of some BAM files from UWash, supply the sample information for each read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3340 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 15:17:05 +00:00
4a7902bb8e
Bases 'A' and 'a' (etc.) no longer considered different.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3339 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:53:38 +00:00
ec543b7b62
The Complete Genomics confusion matrix rates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3338 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:52:10 +00:00
b223b04331
Don't list '.' as an alternate allele, dummy!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3337 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:51:18 +00:00
98718d0faa
Computes the error rate per cycle
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3336 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:50:22 +00:00
7527f950d1
Computes the quality score distribution per readgroup (one column per readgroup)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3335 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:49:38 +00:00
c111c15072
Computes the distribution of insert size per library (for now, one output file per library)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3334 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:48:35 +00:00
a51bd57566
First version of the smart batch merging tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3333 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 02:18:48 +00:00
33a9549896
Variant Optimizer accepts a dbSNP rod arugment to use in determining known/novel status as opposed to using the rsID in the vcf record. VO generates plots of annotation values used in clustering broken out by knowns and novels. Useful for showing which annotations are approximately Gaussian.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3332 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-09 16:48:07 +00:00
76efa757f0
Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder
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which improved startup time 5-10x when dynamically merging many BAMs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3331 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-08 14:12:22 +00:00
504103bd15
Misc. additions to correct utilities
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3329 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 21:34:18 +00:00
64ccaa4c6a
Walkers and integration tests that calculate and compare callable bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3328 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 21:33:47 +00:00
d070554329
A walker that calculates read lengths, number and size of clipping events
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3327 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 21:32:51 +00:00
1749a49042
Mapping and base quality thresholds for DoC default to none
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3326 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 18:08:13 +00:00
7d2df3f511
example windowed ROD walker for Kristian, and updates to Tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3325 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 17:12:50 +00:00
57f254b13a
VE integration test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3324 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 13:58:25 +00:00
44de92e09d
Checking in the liftover script. I am including a post-processing walker to filter out bad records written in under 10 minutes as per my agreement with Mark.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3321 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 12:31:56 +00:00
18f1d31a22
Moving to and organizing in core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3320 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 04:05:36 +00:00
06ea65e60b
again for JIRA GSA-320
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3319 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 03:47:58 +00:00
ac9b32db88
a bug fix for Kiran; putting JIRA in for better type determination system for the new Tribble tracks so this doesn't happen again.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3318 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 03:31:43 +00:00
4e0019b04f
Repair code that sorts and merges intervals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3317 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 22:37:25 +00:00
72e030a670
require that snps be biallelic before we pass them to the TiTv calculation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3316 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 22:33:00 +00:00
7cecec7d00
Removing zero no-calls restriction in AC stats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3314 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 18:55:07 +00:00
0e58fb7cc0
Moved over to be a walker inside the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3313 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 18:28:03 +00:00
78409dca0d
turned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3312 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 16:36:58 +00:00
bacc507a48
Don't worry about sorting anymore in the liftover tool. That will come later.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3311 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 15:00:30 +00:00
5df0361bd2
trivial removal of unnecessary comments
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3309 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 03:51:14 +00:00
2975e3a4e8
picard Intervals don't sort right - switching to GenomeLocs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3308 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 03:50:28 +00:00
1a99fb9318
First pass at liftover tool. Passing buck over to Aaron...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3306 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 20:38:19 +00:00
a0d71540df
speed-up for VCF, adding code to the VCF reader to automagically make an index if one doesn't already exist, and a change to the VCF writer unit test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3305 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 20:19:42 +00:00
6bbcc47b5d
removing some out-of-date RODs and some unused genotype writer formats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3304 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 19:07:13 +00:00
c998c48a23
adding code to detect out-of-date index files, which we now remove and regenerate if the target file is newer than the index file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3303 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 17:55:36 +00:00
a68f3b2e9c
VCF moved over to tribble.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3302 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 17:28:48 +00:00
ad11201235
adding more ROD pile-up tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3301 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 16:01:11 +00:00
0338345bee
Fixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3300 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 15:42:27 +00:00
64640d6b17
Complete the switch statement to deal with all possible cigar operators for Kris.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3299 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 13:41:05 +00:00
f75e54e3f7
fixes for new package names in tribble 74
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3298 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 05:47:04 +00:00
617542853f
Walker that can be used with refGene and a TCGA bed file to annotate intervals in an interval list with the genes and exons they overlap.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3296 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 02:55:01 +00:00
354262eabe
New convenience methods to rodRefSeq for dealing with intervals that may be a superset of multiple exons. Needed for next commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3295 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 02:54:18 +00:00
03bea70f3a
Fixed edge case bug in cleaner: when no -L argument is used and a target interval abuts the end of the reference genome, we'll NullPointer at the first unmapped read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3293 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-04 16:49:21 +00:00
510b3efcc2
Fixed an issue where asking for the alternate alleles at hom-ref sites would result in an array out-of-bounds exception.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3292 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 18:46:33 +00:00
94b51de401
HLA caller updated to examine class II loci, updated pointers to dictionary, allele frequencies.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3290 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 14:54:52 +00:00
97fdd92e7b
Clean up the code to have a unified approach to calculating p(true) for both with and without ti/tv models
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3289 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 13:30:20 +00:00
f497213933
DbSNP moved over to tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3288 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 06:02:35 +00:00
9d01670f62
Major update to the Variant Optimizer. It now performs clustering for both the titv and titv-less models simultaneously, outputting the cluster files at every iteration. It makes use of the Jama matrix library to do full inverse and determinant calculation for the covariance matrix where before it was using only approximations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3286 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-02 19:21:23 +00:00
a318b1871d
Removed unused column
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3285 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 21:29:34 +00:00
9dff578706
Added PG tag to bam header to let people know it's been cleaned.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3284 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 17:30:30 +00:00
0e10359a5e
Okay, finished up the ability to cap a base's qual by its read's mapping quality.
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This is experimental - I have not tested its performance on SNP calling, or even played around with it. If you want to test it out, go nuts. But don't come running to me if your results are not good.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3282 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 16:58:30 +00:00
850f36aa61
Changes to the Unified Genotyper's arguments:
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1. User can specify 4 confidence thresholds: for calling vs. emitting and at standard vs. 'trigger' sites.
2. User can cap the base quality by the read's mapping quality (not done yet).
3. Default confidence threshold is now Q30.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3281 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 16:44:24 +00:00
8b2ce128b5
Optimized the join(..) method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3280 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:55:07 +00:00
8bb15ef812
Checking in the reference implementation of the downsampler for back comparison.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3278 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:41:13 +00:00
1714c322c2
Reorg of UG args; checking in first before upcoming changes that will break integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3274 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 14:48:46 +00:00
ba78d146ec
Finished implementing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3273 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 14:14:31 +00:00
5d5c7f9d34
Changed short code of stop codon to 'stop'
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3272 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 13:55:52 +00:00
cbed0b1ade
Adding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3271 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-29 22:50:17 +00:00
7fbfd34315
adding the GELI ROD validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3270 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-29 21:43:00 +00:00
82818a417b
Allow header fields to come in any order...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3269 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-29 18:33:10 +00:00
4617abf1ff
Fix bug in the interval sharder in cases where contigs specified in intervals are not present in any supplied BAM file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3268 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 20:42:04 +00:00
e2ff4167af
Added "#Family ID" as a possible header value for PlinkRod ... since that's in the new sequenom headers for pilot 3 validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3266 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 18:38:33 +00:00
5dce16a8f1
Better genotype concordance module. Code refactoring for clarity (please see below/after for educational purposes). Now reports variant sensitivity, concordance, and genotype error rate by default. Also aggregates this data across all samples, so you get a per sample and overall stats for each of these in the allSamples row.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3265 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 13:10:11 +00:00
64c5f287c5
fixes for edge-cases when using reflections to find classes outside of the main jar. Will push as a patch to reflections
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3264 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-27 17:46:46 +00:00
c647153b10
Adding Jama for Ryan.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3262 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-27 14:30:36 +00:00
f6468f9143
a fix for a bug we've worked around in the reflections package: previously it didn't find classes that weren't in the main jar. Fixed in this version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3261 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-27 04:49:49 +00:00
df31eeff9f
minor change
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3259 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 06:05:29 +00:00
68bdac254b
a utility walker for validating changes made to the underlying ROD system in the transistion to Tribble.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3258 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 05:21:24 +00:00
d9bf441391
Have UG emit calls at sites from one or more 'trigger' tracks when provided
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3257 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 05:04:43 +00:00
8f2bfac7a6
Bug fix for NullPointerException
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3256 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 05:02:09 +00:00
f5a3b128c8
Fixing bug that's not caught by integration tests:
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If the first eval seen has one or more no-calls, then that's the 2N chromosome count that gets set as the max for the metrics. Instead, just check that any eval's no-call count is 0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3255 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 02:40:34 +00:00
29ab59a7b3
Bug fix for Kiran; insertions now get a null reference allele even if the ref input object is null
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3254 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-24 21:31:03 +00:00
c8d09a29ed
some quick changes to the VE output system - more to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3253 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 21:55:08 +00:00
7f4d5d9973
Ti/Tv by AC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3252 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 17:56:29 +00:00
42bcca1010
Pulling out the left-alignment code for indels so that other walkers can use it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3251 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 16:12:34 +00:00
9e28e4eb42
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3250 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:50:09 +00:00
10bcd72593
1st attempt to implement extra columns
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3249 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:49:37 +00:00
a72a5a7b1a
Data object for representing a single amino acid
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3248 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:49:06 +00:00
e7c0ded40e
Fixed long-standing bug in GenotypeConcordance module of VariantEval which caused incorrect numbers to be displayed in the concordance table. The format of the concordance table has changed. Added a concordance summary table which gives overall genotype concordance summary stats by sample. None of the VE integration tests contained genotype information so I added a comp track with genotypes to one of the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3247 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:48:41 +00:00
e0b51d0df0
Trigger cleaning of duplicate reads. Also beeter debug output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3246 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:12:28 +00:00
3adf7fbf64
bug fix for known-indels used as consenses
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3245 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 13:52:51 +00:00
f050beada6
make sure we do delete the temp file we create
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3244 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 05:32:49 +00:00
536f22f3bd
adding VC adaptor for GELI, along with unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3243 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 05:28:39 +00:00
3d2c836db6
Bug fix for case sensitivity
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3242 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 03:08:58 +00:00
8c94df6f00
Bug fix for Chris: deal with sites that have "semi-deletions"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3241 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 18:34:41 +00:00
121163dd49
interim commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3240 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 13:44:45 +00:00
f0fe2ea530
A simple codon -> AA lookup table
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3239 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 12:18:00 +00:00
e643a9e7a5
Takes a refGene table ( -B arg must be: -B refgene,AnnotatorInfoTable,/path/to/refgene_file.txt) and generates the big table of nucleotides containing annotations for each possible variant at each transcript position (eg. 4 variants for each position).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3238 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 12:11:19 +00:00
653e08c0b6
Takes a refGene table ( -B arg must be: -B refgene,AnnotatorInfoTable,/path/to/refgene_file.txt) and generates the big table of nucleotides containing annotations for each possible variant at each transcript position (eg. 4 variants for each position).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3237 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 12:11:03 +00:00
20379c3f82
Added location-caching optimization, temporary attributes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3236 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 11:35:45 +00:00
84ebceb9a6
Fix for Chris: need to use the appropriate conversion method. Added a warning to the adaptor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3235 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 02:05:10 +00:00
e7334ec11f
Checkin for Eric (IndelDBRateWalker is a prelude to a VariantEval module for comparisons for indels)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3234 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 00:40:27 +00:00
32d86cf457
Rev the reservoir downsampler to support partitioning through a functor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3232 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 19:50:26 +00:00
ef6d900eb8
for now, set log error to -1
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3231 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 19:21:06 +00:00
e9e844fbf5
1. Reverting: dbsnp automatically is a comp
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2. Fixing logic for min Qscore calculation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3230 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:51:35 +00:00
532263ea25
Oooops, forgot to update the test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3229 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:38:24 +00:00
1373fee278
Because of the ugly VCF format, generic addCall() method of GenotypeWriter interface acquired an additional parameter, explicitly specified reference base (in VCF it's the base immediately *before* the event in case of indels, so we got to pass it). All implementing classes are modified to accomodate the change.
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VCFGenotypeWriterAdapter now explicitly uses the passed reference base instead of deriving it from VatriantContext (in SNP mode as well!), other writers simply ignore that additional argument.
SimpleIndelCalculationModel now WORKS (or rather, it does produce calls :) )
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3228 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:19:03 +00:00
ab34397d2e
Continuing to stamp out the non-ASCII copyright virus.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3227 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 14:50:45 +00:00
84f1ccd6ac
Two dumb oneoff walkers written to fix & annotate the Baylor indel calls (which came in sans reference, and without coding/intron annotations).
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ERIC -- does the IndelAnnotator (the RefSeq lookup code I stole from IndelGentoyperV2) want to be its own Annotation inside VariantAnnotator? Is Andrey already doing this as part of adding indel calling to UG?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3226 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 14:04:10 +00:00
2fdc1cf490
Bed ROD track support
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3225 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 13:22:42 +00:00
51b3998082
deleting unused code from VariationFiltration
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3224 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 13:22:19 +00:00
4abd3b0b7b
Fixing known/novel calc now that dbsnp isn't a default comp track
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3223 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 05:43:59 +00:00
114819d980
Allow user to set min confidence score for comp tracks too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3222 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 05:09:09 +00:00
3db73e0791
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3221 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 03:00:43 +00:00
3b5673d967
1. Removed -all; by default all modules are used; use -none for no modules.
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2. Don't make dbsnp track be a comp by default (to cut back on output). Please let me know if someone wants this back for some reason.
3. Cleaned up dbsnp module output to print the right numbers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3220 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 02:46:42 +00:00
4e18c54bb8
fixing a couple of commented out portions of the VCFReader test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3219 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 22:20:35 +00:00
6fda78f93f
Always return deleted bases in upper case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3218 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 19:17:40 +00:00
52a570637d
Always keep event bases in upper case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3217 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 19:16:39 +00:00
80c4f88a72
removing the Variation interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3216 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 18:56:45 +00:00
7d952a34ae
Fixing copyright note
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3215 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 18:28:57 +00:00
cdc175f7e3
Synchronizing version to make sure everything compiles; this model is not operational yet
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3214 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:41:52 +00:00
4437456bb5
Pass array of ref bases to callExtendedLocus()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3213 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:41:13 +00:00
5d2fab93f4
Method signature changed: for extended events, pass array of reference bases (to ensure we cover the full length of the indel event), not just reference base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3212 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:40:30 +00:00
01e6492ba9
Updated to work correctly with extended pileups. Clogged and uses some dirty tricks; pileups/extended pileups need to be redesigned someday
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3211 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:38:09 +00:00
4723cad1be
New method: getBasesAtLocus(int n); for the windowed reference context, this method extracts n bases starting at the current locus (NOT at the window start, so this method is an extension of getBase())
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3210 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:35:09 +00:00
cac125b35c
Fixed incorrect symbol printed into the output file (tag had 'R', should have had 'T')
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3209 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 16:37:28 +00:00
f4977965b6
Removing debug statements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3208 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 16:22:40 +00:00
124b7a2a58
Moved ApplyVariantClusters over to VariationContext
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3207 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 16:20:25 +00:00
200d3e2c47
added copyright note
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3205 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:44:26 +00:00
546dfb629e
A draft (working) version of a tool that computes per-cycle base qualities averaged across the reads; the computed base qual profiles are stratifeid by lane/read end and separately by library.Come and shoot me if we already have such a tool somewhere in the repository :)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3204 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:38:16 +00:00
c1e53d407d
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:26:32 +00:00
b5f6f54968
Almost done removing any trace of the old Variation and Genotype interfaces.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3202 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 14:52:15 +00:00
818a95ea6e
Test of new copyright message without unicode characters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3200 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 14:14:54 +00:00
00feb3eee0
Moving over to VariationContext in CountCovariates. Removed references to class Variation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3199 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 13:26:22 +00:00
1bc26f69e9
An attempt to cleanup the Utils directory. Email to follow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 23:00:08 +00:00
c08936d6f4
Added a reservoir downsampler which can sample elements in an iterator uniformly
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from a stream (see Vitter 1985). Thanks to Eric and Andrey for the pointer.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3197 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 20:48:14 +00:00
c44f63c846
Fixing the performance tests: we need to catch the RuntimeException (not samtools' RuntimeIOExcpetion). Also, CountCovariates doesn't need the catch.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3196 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 14:28:12 +00:00
abf48cee05
Moving over to VariantContext from Variation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3195 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 06:56:29 +00:00
d73c63a99a
Redoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it.
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Also, adding some more useful integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3194 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 05:47:17 +00:00
131703d9db
more clean-up: moving AlleleBalanceInspector to archive.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3192 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 20:53:33 +00:00
534f24177a
Move to VariantContext and improve performance (and ease of use) by transitioning to be a RODWalker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3191 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 20:09:48 +00:00
8c32bb8f0a
Complete the move over to VariantContext so that we can remove dependence on Variation (in the VCF code)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3190 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 19:41:42 +00:00
821e8b1c5f
more cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3189 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 19:16:16 +00:00
e11ca74eb5
removing some outdated ROD classes (PooledEMSNPROD and SangerSNPROD), removing an out-of-date interface (VariantBackedByBenotype), and moving AnalyzeAnnotationWalker over to VariationContext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3188 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 18:59:29 +00:00
d5e5589b8f
No longer used
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3187 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 17:57:39 +00:00
be7cbf948b
adding a catch for the exception thrown by samtools when it attempts to close /dev/null in the performance tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3186 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 17:41:48 +00:00
4d75b26b7a
Removing the code that made the ROD system case insensitive. Anyone using specific ROD names in their classes should take care in naming required tracks; All lowercase is the best practice.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3184 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 06:17:31 +00:00
6dc1275cfb
Utility method added: getQualsInCycleOrder(read) - examines the read and returns its quals in the order the machine read them (i.e. always from cycle 1 to cycle N). Simply inverts quals if the read happens to be rc-aligned :)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3183 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 00:15:57 +00:00
f4673efd2f
Moving to archive as it's no longer supported
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3182 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 22:10:42 +00:00
02a6f4c401
Moving over to VariantContext
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3181 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 22:07:28 +00:00
7adff5b81a
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3180 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:36:19 +00:00
e702bea99f
Moving VE2 to core; calling it "VariantEval" (one more checkin coming)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3179 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:25:47 +00:00
ac6f6363ce
Execs() temporarily disabled after removal of bam file. New tests forthcoming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3178 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:11:56 +00:00
ac9dc0b4b4
Removing VariantEval (v1); everyone should be using VE2 now. Docs coming ASAP.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3177 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 19:53:02 +00:00
3330e254a9
Standardize the dbsnp track name in preparation for case-sensitivity
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3176 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 19:41:57 +00:00
5f7564bf0a
Better naming of output columns
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3175 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 18:08:07 +00:00
e682460c1f
add a fix so that XL arguments won't cancel out -BTI arguments, fixed a bug for Ben where the ROD -> interval list conversion was throwing an exception, and some old code removal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3174 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 16:31:43 +00:00
b54031fc86
adding an experimental format to VariantEval2, which when you source() from R, imports all VE2 output as individual tables with appropriate row and column names. More testing and feedback needed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3172 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 06:09:27 +00:00
04909fa6ad
Removing arbitrary selects
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3169 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 17:46:39 +00:00
f1189bac5a
Bug fix: final map call wasn't being triggered (because we returned when ref==null before applying update0)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3168 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 16:58:55 +00:00
b930dc52a5
Integration test for GenomicAnnotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3167 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:43:25 +00:00
c0f4695902
Improved handling of haplotypeReference and haplotypeAlternate columns. Added haplotypeStrand column. Improved handling of empty fields in data files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3166 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:42:19 +00:00
74ec72d1ac
Added AnnotatorROD - the TabularROD format specific to GenomicAnnotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3164 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:39:50 +00:00
77a6608784
Changed a variable name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3163 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:38:18 +00:00
7b8056099c
Fixed 'N' reference-base handling, changed some comments, var names
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3162 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:37:25 +00:00
dde092fb61
Added the ability in VE2 to select which eval modules to run, so that you aren't forced to use all of them. You can use --list to list all of the possible modules to run.
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Heads up everyone: by default, *no* modules are run. Please add "-all" to your scripts to maintain the previous behavior.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3161 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 22:15:58 +00:00
0b575596f8
Fix for concordance: samples found only in truth no longer kill it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3160 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 21:33:49 +00:00
8573b0bc6f
Refactoring intervals, separating the process of parsing interval lists,
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sorting and merging interval lists, and creating RODs from intervals. This
gives Doug the ability to keep using our interval list parsing code when
sorting intervals on our behalf.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3159 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 15:50:38 +00:00
d0123956bc
Modified comments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3158 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 15:41:59 +00:00
7b05091c04
DoC now does not require a -o argument. (Change for Matt)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3157 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 13:58:17 +00:00
e413882302
Generalizing the SequenomValidationConverter to be able to take in any arbitrary rod type (provided it can be converted to VariantContext).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3155 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-12 20:42:18 +00:00
14b8101d45
Error message fail. Failed to supply one of the valid interval file types.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3153 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-12 01:19:01 +00:00
60d54e69f3
Hackish fix to present a better error message if the file does not have the proper extension. Will work with Brett to come up with a better solution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3152 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-12 01:11:27 +00:00
d06c7835d8
Adding performance tests for the indel realigner; should take ~3 hours.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3151 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-11 04:45:22 +00:00
3434a61146
Don't trigger when ref=N (which can happen when a dbsnp track is provided)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3150 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-11 02:59:11 +00:00
961ca05abc
Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3149 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-11 01:43:07 +00:00
fa01876255
UnifiedGenotyper performance tests (WG, WEx); currently takes just over an hour.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3148 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 19:42:29 +00:00
0cc6d0fbbb
One more quick memory improvement: reuse Alleles in a given context instead of creating new ones for each sample (duh).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3147 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 18:48:36 +00:00
c2a37e4b5c
Variant Quality Score modules in VariantEval2 no longer create huge lists which hold all of the quality scores encountered and instead cast the quality score to an integer and use hash tables. Bug fix for files in which all the quality scores are set to -1.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3146 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 18:36:06 +00:00
71f38a9199
Adding performance tests for the recalibrator (Whole Genome and Whole Exome tests).
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Should take ~3 hours to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3145 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 18:30:59 +00:00
e73e6a4fb0
Significant memory improvements to plink code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3144 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 16:12:38 +00:00
f1b1e70612
Bug fix for multisample calls in ApplyVariantClusterWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3142 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 12:01:15 +00:00
3f2455e346
Better error message as suggested by James P
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3141 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 05:52:53 +00:00
fba48b515a
Heads up everyone:
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For consistency, these tools should be writing to the walker's output stream and no longer use the -vcf argument.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3140 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 05:37:25 +00:00
e286623f6f
Use byte[] instead of String in an attempt to cut down on memory usage
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3139 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 05:32:54 +00:00
7025f5b51d
Added an auxiliary table to DepthOfCoverage, which is the cumulative equivalent of the locus table (got tired of doing the calculation by hand). Also took care of a trailing tab in the per-locus output table.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3138 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 19:37:17 +00:00
9f6377f7fb
added a performance test build option (for the upcoming performance test suite), and added a sample performance test for VariantEval.
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IMPORTANT: it was really redundant that we had -Dsingle and -Dsingleintegration to run single unit tests and integration tests, now you can just use -Dsingle to run a single test for performance, unit, and integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3136 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 15:37:15 +00:00
4014a8a674
A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.
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Thanks!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 06:14:15 +00:00
e148a3ac61
added the ability to create interval lists directly from a ROD, using the command line arg '-BTI' (long name '--rodToIntervalTrackName'). The parameter to this arg is the name of the ROD track, which must be a track name specified in the -B option.
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Using this feature, sites covered by the target ROD will be iterated over. This list of intevals generated is merged with any intervals from the -L and -XL args, and the Walker is run over the resulting merged list.
WARNING: for very large ROD's this can be costly. Consider this experimental for now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3134 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 05:14:41 +00:00
20cc2a85a4
removed the hashmap from Genotype Concordance, moved it into a table
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3133 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 21:24:48 +00:00
e55f27b3b1
forgot a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3132 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:51:13 +00:00
9ca8e345fc
by-by old junk.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3131 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:41:48 +00:00
8fd59c8823
Modified the report system based on Ryan's feedback: tables are now created independently to avoid the permutation problem when they were all compressed in rows, and removed our dependency on FreeMarker. The Grep format stays the same.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3130 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:39:55 +00:00
918b746798
More detailed validation output. Fixes for genotyping overflow -- these are temporary and need to be properly resolved
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3129 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 16:38:28 +00:00
e7dad728df
Trivial output changes for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3128 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 14:47:43 +00:00
058e7d3d12
Bug fix for Gregory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3127 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 00:21:35 +00:00
7b44e6bd55
ApplyVariantClusters now outputs interesting threshold points based on hitting the target novel TiTv
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3126 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 19:47:29 +00:00
60c227d67f
Added new VE2 module to create a plot of titv ratio by variant quality score
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3125 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 15:19:27 +00:00
3530ef5a41
Explicit type cast fixed in order to work with new ROD implementation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3124 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 15:02:56 +00:00
2d002c56c3
Added histogram of variant quality scores broken out by true positive and false positive calls to the GenotypeConcordance module of VariantEval2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3123 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 13:48:31 +00:00
12e4f88ca7
a little bit more clean-up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3122 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-05 20:49:06 +00:00
df7e7921ce
removing some unused code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3121 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-05 19:30:08 +00:00
56eb15f91f
Error checking for bad input (thanks, Aaron).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3120 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-04 03:17:01 +00:00
705b28e90d
First attempt at implement record filtering based on special 'hap_ref', 'hap_alt' columns in the input files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3118 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 21:52:26 +00:00
d78e7f6c0a
Added documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3117 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 21:51:28 +00:00
8017fb123f
changed the depth of coverage walkers class name, and added a dependency in the packaging system so that RODs will all get imported.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3116 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 20:55:19 +00:00
6b7b07f178
First checkin of GenomicAnnotator which annotates an input VCF file by pulling data in a generic way from an arbitrary set of TabularRODs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3114 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 17:49:42 +00:00
642c969896
reverting optimizer changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3112 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 16:59:13 +00:00
d7880ef7ad
Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3110 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 17:17:16 +00:00
f7d1b8f5de
CoverageStatistics has now replaced DepthOfCoverage -- old DoC is in the archive.
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Also, I can't be bothered to fix the spelling of "oldepthofcoverage" to contain the necessary number of D's. Be content that it does, however, contain the requisite number of O's.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3109 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 16:27:23 +00:00
585cc880a2
changed jexl expressions to jexl names in the VariantEval2 output, fixed integration test, and fixed a problem where a line was getting dropped in CSV output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3108 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 16:23:14 +00:00
d00bde22db
Reverting one of Brett's changes that should not have been committed. Will
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address with Brett separately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3107 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 16:10:46 +00:00
b4f6f54502
Reorganizing the way interval arguments are processed
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Most of the changes occur in GenomeAnalysisEngine.java and GenomeLocParser.java:
-- parseIntervalRegion and parseGenomeLocs combined into parseIntervalArguments
-- initializeIntervals modified
-- some helper functions deprecated for cleanliness
Includes new set of unit tests, GenomeAnalysisEngineTest.java
New restrictions:
-- all interval arguments are now checked to be on the reference contig
-- all interval files must have one of the following extensions: .picard, .bed, .list, .intervals, .interval_list
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3106 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 12:47:48 +00:00
c3c6e632d1
support for two new VCF header info field value-types, Flag (for fields that are just boolean truths), and Character (for single charatcer info fields).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3105 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 03:11:32 +00:00
3d3d19a6a7
the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.
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a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects. This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc. This layer is needed so we can integrate Tribble tracks (which don't natively have names). Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc).
Sorry for the inconvenience! More changes to come, but this is by far the largest (as has the greatest effect on end users).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3104 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 22:39:56 +00:00
4fcee248f9
For Kristian: functions which, given a read, can uniquely identify the BAM file storing that read.
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Introducing this into the pile of code which peeks under the covers of the SAMDataSource in the hopes
that this function can help to replace the others and provide a single path for crosstalk.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3103 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 20:46:44 +00:00
d58fe70708
Correctly ignore filtered calls and indel calls in the truth sets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3101 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 14:33:01 +00:00
b60197ae10
Another round of cleanup and simplification in Picard -- Picard's unit tests
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are now passing for my branch.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3100 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 01:02:59 +00:00
40f8e7644c
Better, multi-haplotype aware haplotype scores. Looking very good now, seems to be vastly better at dealing with incorrect calls in deep and low pass data. Almost ready for use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3099 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 23:57:36 +00:00
f992f51a3b
Deleting incorrect sampling genotype likelihoods from the codebase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3098 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 23:56:35 +00:00
b9d3fc3fbb
Now checks if the i-th element of the FiltrationContext[] is null before trying to access it. This seems to happen occassionally at the very end of a VCF file... the array will be 6 elements long, but the last element will actually be null.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3097 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 22:40:17 +00:00
400684542c
Revisions to take into account finalization of Picard patch: naming changes, better definition
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of public interfaces. This won't be the last Picard patch, but it should be the last big one.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3096 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 19:28:14 +00:00
b00d2bf2bc
fixing an annotation that was breaking the error log output system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3095 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 15:34:04 +00:00
a6e8687d71
implementing a clean way to import the template files into the GATK jar (they should not always get bundled). All further resources should be added to the gatk.resources path id in the build script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3094 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 04:20:19 +00:00
babb9fb825
snp cluster filter should ignore ref calls when determining the clusters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3093 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 17:57:33 +00:00
24461a2503
Let's *not* import classes that no longer exist. How my own ant test compiled is beyond me.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3091 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:59:01 +00:00
dc802aa26f
Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3090 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:32:00 +00:00
1e8b3ca6ba
Fare thee well, oh LocusWindowTraversal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3089 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:17:26 +00:00
8ea98faf47
Deleting the pooled calcluation model -- no longer supported.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3088 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 11:44:27 +00:00
85037ab13f
Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of
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Picard patch, including move of some of the Picard private classes we use to Picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 03:21:27 +00:00
a45ac220aa
Removing unnecessary printing routines
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3086 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-28 22:34:54 +00:00
b8ab74a6dc
Minor useful changes to BaseUtils and MathUtils to support a new haplotype score annotation that determines to the two most likely haplotypes over an interval and scores variants by their consistency with a diploid model. Appears to be useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3085 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-28 21:45:22 +00:00
e9e53f68ab
Filter lists can now end with .list or .txt.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3084 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-27 17:41:24 +00:00
kshakir
chartl
ebanks
hanna
aaron
flannick
depristo
rpoplin
kiran
fromer
asivache
delangel
bthomas
weisburd
sjia