3e54e131e0
Cleanup and formatting overhaul.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2652 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 19:22:56 +00:00
ee421c106c
Autogenerate .tar.bz2 with embedded version number. Misc formatting changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2651 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 18:32:46 +00:00
f51cffe220
Alteration of PlinkToVCF to be much more flexible about parsing .ped file headers, which can have one of a number of different standard fields, and be in different orders.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2650 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 18:02:28 +00:00
5b2a1e483e
Renamed SequenomToVCF as PlinkToVCF. Wiki will be changed accordingly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2649 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 17:35:20 +00:00
74779a9a78
First version of the tool that tries determining indel error rate (basically, counts indels that look like sequencing/alignment errors - such as a single observation at deeply covered locus, and reports the rate of their occurence)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2648 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 15:28:20 +00:00
d25a2fe120
Better handling of enums by the command-line argument system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2647 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 21:36:46 +00:00
9c7b281b4f
Set default value for max_coverage to be 100K (since 10K is too small).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2646 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 20:15:25 +00:00
1e9fe2a334
Clean up error output when enums have missing arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2645 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 19:48:26 +00:00
8d1d37302c
a quick change to GLF to keep as much precision in our likelihoods as long as possible, before we put it into byte space. Sanger was doing a diff at low coverage and noticed our calls didn't contain as much precision as theirs. Updated the MD5 for unified genotyper output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2644 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 19:36:49 +00:00
908d399670
Bug fix for help text / version number - help text retriever was crashing in the debugger if help text hadn't been built.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2643 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 19:18:19 +00:00
ab289872e4
Changes:
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- Annotations return null when given pileups with no second-base information
- SequenomRodWithGenomeLoc -- beter handling of indels
Eric; I made two small changes to the new Genotype interface that we should talk about (they basically have to do with allele/genotype representation):
Allele - added a new UNKNOWN_POINT_MUTATION to AlleleType. If I see a sequenom genotype AG; one's got to be ref, one's got to be SNP, but until I have
an actual reference base in hand, I don't know which is which. That's what this entry is for.
Genotype - added an enum class StandardAttributes for dealing with things like deletion/inversion length. This is probably not the way we want to
represent indels, so we should talk about this. Plus now that there's a direct link between my ROD and the genotype; when we do decide
how to deal with indels, we'll be forced to alter the SequenomRodWithGenomeLoc accordingly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2642 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 16:45:17 +00:00
cf46e3c85f
Valuable series of commands
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2641 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 13:58:59 +00:00
a1b4cc4baf
changes to intelligently log overflowing locus pile-ups.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2640 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 08:09:48 +00:00
4ac9eb7cb2
- Smarter strand bias calculation
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- Better debug/verbose printing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2639 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 03:01:26 +00:00
2261f57e5c
Rename modules to reflect the fact that they're really packages in their own right.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2638 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 01:13:17 +00:00
2f3fbc145d
A rethink of some of the modules from last night -- make the modules stand alone.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2637 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 00:59:21 +00:00
ff66023d83
Trivial change to support filter field in VCF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2636 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 22:56:22 +00:00
4625261d79
Bug fix: alignments ending with 'I' were not counted into the overall coverage which resulted in inaccurate stats, and in rare occasions outright messed up ones.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2635 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 22:12:16 +00:00
96a053c769
Port VariantEval and FindContaminatingReadGroups to modules.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2634 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 22:10:33 +00:00
8dafd26100
Print out the current version number in the application header.
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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%)
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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.
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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.
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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.
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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.
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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
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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.
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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.
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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.
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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.
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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
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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
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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
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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
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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
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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.
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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
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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
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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
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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.
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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
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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
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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.
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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.
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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
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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.
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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
hanna
chartl
asivache
ebanks
aaron
depristo
kshakir
rpoplin
kiran
mmelgar