8dafd26100
Print out the current version number in the application header.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2633 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:58:36 +00:00
9e0ae993c7
-B 1kg_ceu,VFC,CEU.vcf -B 1kg_yri,VCF,YRI.vcf system supported to allow 1KG % (like dbSNP%)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2632 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:33:13 +00:00
e936cbff1b
Removed experimental recalibration covariates.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2631 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:29:43 +00:00
c98df0a862
Updated solid_recal_modes to work with bfast aligned data. Added an integration test that uses the BFAST file provided by TGen.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2630 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:18:02 +00:00
53352e1bb4
First pass at a sequenom ROD. Nothing uses it; currently undergoing testing.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2629 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 17:09:36 +00:00
1488578617
Working with Aaron to get svnversion running within the build system. This change will break the build.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2628 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 16:55:42 +00:00
bca436578f
Added the -maxQ argument to the list of arguments in the PG tag
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2627 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 15:55:23 +00:00
d61cafd19f
Make the formatting of the list of args in the PG tag consistent.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2626 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 15:31:37 +00:00
a12465b6d5
The recalFile argument is no longer added into the PG tag of a bam produced by TableRecalibration. Based on a request from the Sanger.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2625 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 15:25:57 +00:00
e1fba42fdb
Add new 'module' XML tag, that can import modules from supplementary files.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2624 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 01:56:04 +00:00
ba19afd529
Draft version of AnalyzeAnnotations which creates plots of cumulative TiTv ratio versus filter value per each annotation in the input VCF rod. Minor cleanup of recalibration walkers.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2623 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-18 20:47:10 +00:00
ff6877a15e
Added a forgotten column label
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2622 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-18 01:00:52 +00:00
dd6d5aadf9
Computes empirical confusion matrices, optionally with up to five bases of preceding context
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2621 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-18 00:55:12 +00:00
12453fa163
Misc cleanup of UG args
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2620 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-17 04:38:52 +00:00
a57886ab81
Adding VCFValidator to package
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2619 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-17 03:39:05 +00:00
b8cdf64c20
Better descriptions for max reads/downsampling args
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2618 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-17 02:30:27 +00:00
aa08c82ac0
Removed experimental covariates and added standard annotations.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2617 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-17 02:17:32 +00:00
8226f4aa12
minor cleanup
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2616 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 20:23:20 +00:00
d8e74c5795
Update to MD5s for old tests and added extensive VCF testing
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2615 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 20:22:58 +00:00
64225b28fd
Convenience methods for getting the VCFReader and VCFRecord
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2614 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 20:22:31 +00:00
d0af7f6c7b
Now analyzes filtered SNP like all, novel subsets; support for selecting a single sample to analyze from a multi-sample VCF, support for trivial selection of records with INFO field key/value pair.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2613 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 20:22:04 +00:00
8ae8e120f8
New annotateUnion operation -- provides clearer annotations on where a call came from when unioning two VCF call sets
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2612 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 20:20:37 +00:00
41392f8ff5
functions for setting gentoype records and alternate bases; function for getting all rods implementing VCF
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2611 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 20:19:43 +00:00
d2961a3a17
Typo in previous commit.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2610 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 01:41:42 +00:00
45de006ca3
Disable extraction of svn info completely.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2609 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 01:30:25 +00:00
8ce79e002c
Fix for failed build. Seems to be an issue with Bamboo environment. I'll
...
discuss w/ Aaron next week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2608 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 01:06:26 +00:00
ac4756db20
Add the svn version on the fly to the version number properties.
...
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
...
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
...
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,
...
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.
...
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
d30e2b390a
Remove several walkers that won't be used in the GATK-GSA-Pipeline.jar.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2602 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 21:17:23 +00:00
7a991421f7
-erw argument, begone! Rod traversals are now enabled. current tests pass, more tests for RODWalkers are welcome ;)
...
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 ;)
...
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...
...
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
d2f752dbc1
Adding TileCovariate to the GATK-GSA-Pipeline list.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2598 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 20:57:13 +00:00
190335db9c
Added a GSA specific package with Playground walkers.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2597 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 20:50:29 +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...
...
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.
...
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.
...
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
...
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.
...
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 :-/
...
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.
...
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.
...
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.
...
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
...
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:
...
* 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...
...
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.
...
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
hanna
depristo
kshakir
rpoplin
chartl
kiran
ebanks
mmelgar
asivache
aaron