ac4756db20
Add the svn version on the fly to the version number properties.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2607 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 00:28:01 +00:00
420cef4094
Added version numbers to the help doclet extractor. Since the help system is behaving
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more like a resource bundle at this point, changed it over to use the Java ResourceBundle
support classes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2606 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 23:31:29 +00:00
4de7d6a59b
Initial checkin of skeleton code for AnalyzeAnnotations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2605 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 21:52:34 +00:00
930082314a
Put a major.minor version into the GATK Javadoc for reading. Also,
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update some straggler packages to the new package-info.java format introduced in 1.5.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2604 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 21:48:30 +00:00
3063224446
SecondaryBaseTransitionTableWalker now breaks by genotype and read group, is javadoc annotated, and is compatible with ReadBackedPileup's methods.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2603 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 21:43:39 +00:00
7a991421f7
-erw argument, begone! Rod traversals are now enabled. current tests pass, more tests for RODWalkers are welcome ;)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2601 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 21:11:14 +00:00
c8c5c176cd
-erw argument, begone! Rod traversals are now enabled. current tests pass, more tests for RODWalkers are welcome ;)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2600 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 21:07:49 +00:00
a12933a26d
Bug fixed: now the length of an insertion is determined correctly. Thought I committed this...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2599 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 20:58:48 +00:00
404b95183f
This is a LocusWalker, not a RodWalker (thanks Mark!!). RodWalkers currently are not capable of attaching alignment contexts (reads) to the ROD-annotated loci they traverse over...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2596 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 20:33:41 +00:00
7078219b89
Updating outdated comments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2595 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 19:17:52 +00:00
ba2acda406
Clarifying the comment regarding differentiating between first and second of pair in CycleCovariate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2594 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 18:36:14 +00:00
b911b7df82
Fixing the AC annotation to be in line with the VCF spec
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2593 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 18:28:52 +00:00
f2e539c52f
As per discussions with Tim we are reverting the previous change regarding PairedReadOrderCovariate. The CycleCovariate now differentiates between first and second of pair by multiplying the cycle by -1. PairedReadOrderCovariate has been removed completely.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2592 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 18:18:59 +00:00
eae1b73945
Fixed a bug in left-adjusting the indels introduced in previous commit :-/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2591 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 17:41:23 +00:00
df998041a8
Minor change to solid warning message. Added note for a future solid recalibration integration test when we get the required data file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2590 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 16:31:25 +00:00
70df30fc1b
Added method to AlignmentUtils which takes a read's cigar and the refBases char array given to a ReadWalker and returns the aligned reference char array. Bug fix in solid_recal_modes to use this aligned reference array. Recalibrator version number is no longer separate for each of the two walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2589 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 15:36:59 +00:00
2a116bb5d6
Made the VCF validator a simple rod walker instead of having it be in a separate package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2588 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 06:39:06 +00:00
b19bb19f3d
First successful test of new sharding system prototype. Can traverse over reads from a single
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BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2587 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 03:35:55 +00:00
db9570ae29
Looks bigger than it is:
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* Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes).
* Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations. You can now specify:
"-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2586 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 00:14:35 +00:00
cff8b705c0
Oh, and the test would not work anymore...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2585 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-14 17:47:09 +00:00
04fdbbfa65
This is the beginning of a new version of VariantEval that can cut VCF files up in a variety of ways with JEXL expressions, select one sample out of a multi-sample VCF, and can load analysis modules dynamically.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2584 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-14 17:45:58 +00:00
df63f51253
No changes, just sync-ing; only some commented out debugging prints are added...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2583 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-14 17:45:15 +00:00
d85461c463
MergingIterator completely re-done. Now it is not a generic class (sorry guys), but rather it is tailored for merging ROD tracks. This implementation peeks the locations of next ROD annotations in each track, but does not actually read these RODs from underlying streams until the location is reached and it is time to actually return the object. Now underlying ROD track iterators (registered in the resource pool!) are not advanced prematurely past the current position and all the way to the next ROD record wherever it is, so that the sharding system can reuse them.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2582 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-14 17:43:36 +00:00
c0891d512f
added: peekNextLocation(); it's quite hard (and probably unnecessary, ever) to make seekable iterator a peekable one, but it is quite easy and useful to be able to peek just the next location the iterator will jump to after next call to next()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2581 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-14 17:38:19 +00:00
9bf0d7250a
Fixing the testOtherOutput UG integration test so it will run.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2580 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-14 13:40:14 +00:00
a082b948a3
Support throughout for S and N cigar elements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2579 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-14 03:45:42 +00:00
424d1b57f7
Sequenom to VCF now allows user to specify filters for QC, and they will appear in the filter field of the output VCF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2577 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 23:22:37 +00:00
f96b2b211e
My last checkin updating R code broke an unrelated UnifiedGenotyper integration test. Eric says that I should take out the verbose test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2576 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 22:28:10 +00:00
49c44e7b36
PairedReadOrderCovariate is now a standard covariate and because of this CycleCovariate no longer multiplies by negative one for second of pair reads. Added PairedReadOrderCovariate to some of the integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2574 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 20:09:10 +00:00
05575e2e56
Better bounding for the locus window. Don't make the locus window calculation blow up if the GenomeLoc ends
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up being outside the reference. Force the blowup elsewhere.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2573 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 17:03:54 +00:00
8ca5bba738
We emit genotype data in the VCF record if the format string instructs us to (regardless of whether or not genotypes are provided - this was the wrong test).
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SequenomToVCF now correctly has no-calls when probes fail.
Re-enabled SequenomToVCF integration test.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2572 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 15:40:27 +00:00
6d1107a4ed
Update to SequenomToVCF
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Output changing slightly so integration test disabled temporarily
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2571 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 15:32:05 +00:00
f99586f91b
Added integration test for beagle and verbose output in UG.
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Minor cleanup of VCFRecord code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2570 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 03:55:24 +00:00
02e23e2d9c
Threading support for beagle output files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2569 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 02:42:16 +00:00
0513690416
two fixes in the new cached DbSNP code:
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-isBiallelic would incorrectly say triallelic sites are biallelic.
-getAlternateAlleleList was broken, since the new cached list is immutable, we couldn’t remove list items.
Also added a dbSNP validating walker to the one-offs, for testing the new b37 130 dbSNP rod.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2568 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 00:27:34 +00:00
a138bad95a
A rare but not-so-subtle bug fixed: a funky alignment (a kind that should not have been generated in the first place) could make the indel left-adjusting method to overshoot read start and build a cigar like -3M6I...
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also, few minor fix-ups.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2567 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 21:29:50 +00:00
b51f4aae11
Updating the recalibrator to make use of StingSAMFileWriter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2566 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 20:58:27 +00:00
c8ad025ad0
cleaning up unused import statements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2565 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:52:37 +00:00
189829841b
The recalibrator now uses all input RODs when looking for known polymorphic sites not just the one named dbsnp. Added an integration test which uses both dbsnp and an input vcf file and skips over the union of the two.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2564 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:50:39 +00:00
16777e3875
more fixes for the empty interval list problem; you can now run LocusWindow traversals with an empty interval list, but the GATK will give you a warning (unless you're running in unsafe mode).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2563 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:47:43 +00:00
35a4fcc481
Additional sanity checking: make sure the user can't alter the header / compression level / presorted state of a file to which SAMRecords have already been written.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2562 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:39:41 +00:00
03b7d5f5c7
1. Fixed small but embarrassing bug in weighted Allele Balance annotation calculation.
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2. Made RankSumTest abstract; added 2 subclasses: BaseQualityRST and MappingQualityRST (the latter based on a suggestion from Mark Daly). Untested so they're still experimental.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2561 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:33:53 +00:00
58999a8e9d
Enhance the I/O management system to support custom headers and set the presorted flag
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from the initialize() method (or at any time before the first SAM record is written).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2560 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:21:42 +00:00
3c5f5177b1
check to see if the parsed interval list is empty, since we now allow interval files that are empty. If so, make sure we default to a non-interval based traversal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2559 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 17:52:27 +00:00
040fdfee61
Cleaned up the interface to VCFRecord. It's now possible (and easy) to create records and then write them with a VCFWriter.
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I've updated HapMap2VCF to use the new interface; Chris agreed to take care of Sequenom2VCF.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2558 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-11 21:42:12 +00:00
42aff1d2c3
Annotator in general should be able to annotate monomorphic or tri-allelic sites.
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It's up to the individual annotations to decide whether they want to annotate or not.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2556 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-11 19:52:18 +00:00
11f91b3c95
Reverting Eric's previous change because it killed the PG tag in the output bam file header. Added a new -compress command line argument to set the compression level of the output bam file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2555 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-11 19:02:56 +00:00
dfa3c3b875
Added:
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SequenomToVCF - Takes a sequenom ped file and converts it to a VCF file with the proper metrics for QC. It's currently a rough draft,
but is working as expected on a test ped file, which is included as an integration test.
Modified:
VCFGenotypeCall -- added a cloneCall() method that returns a clone of the call
Hapmap2VCF -- removed a VCFGenotypeCall object that gets instantiated and modified but never used
(caused me all kinds of confusion when I was basing SequenomToVCF off of it)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2554 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-11 17:17:21 +00:00
62dd2fa5be
Fixing another bug in solid recal regarding negative strand reads. The isInconsistentColorSpace method incorrectly used the inconsistent tag added by parseColorSpace, the inconsistent tag is in the direction of the read like the color space tag, and not in the direction of the reference like everything else. This affects the recalibrated quality scores but the improvment in SNP calling performance is minor when using the default UG settings (min base quality 10).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2553 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-11 14:28:52 +00:00
971834ca90
Added a walker to the vcf tools compilation: one that combines vcf records. Both merges and unions are supported (see documentation... when it gets written this week).
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Also, moved some code that pulls samples out of rods from VCFUtils into SampleUtils.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2552 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-10 06:45:11 +00:00
hanna
rpoplin
mmelgar
asivache
ebanks
aaron
kiran
chartl