bd11060e72
Ups, I did it again. Fixing the bug introduced in a previous commit: use correct length of the indel event.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2713 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 21:51:54 +00:00
fddca032bb
Initial commit of v2.0 of the cleaner. DO NOT USE. (this means you, Chris)
...
Cleaned up SW code and started moving over everything to use byte[] instead of String or char[].
Added a wrapper class for SAMFileWriter that allows for adding reads out of order.
Not even close to done, but I need to commit now to sync up with Andrey.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2712 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 21:36:42 +00:00
b8ae083d1b
AnalyzeAnnotations creates a plot of dbsnp rate as a function of the annotations.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2711 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 21:08:33 +00:00
3999a8d2c8
IntelliJ no longer complains that my methods are too complex to analyze.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2708 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 20:12:13 +00:00
fc4285f9fd
AnalyzeAnnotations seems to be popular so I've rewritten the guts to be easier to extend and maintain.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2707 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 19:30:31 +00:00
fa3589e5c5
Update our error messages to point to getsatisfaction.com/gsa.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2706 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 19:16:28 +00:00
3399ad9691
Incremental update 2 -- refined allele and VariantContext classes; support for AttributedObject class; extensive testing for Allele class, and partial for VariantContext. Now possible to easily convert dbSNP to VariantContext.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2705 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 17:19:37 +00:00
3edcefb7fb
add _gI and _gD to the indel probe names according to the spec (in the hope that wiki is not obsolete); added optional cmd line param -project_id to prefix all probe names with.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2704 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 17:06:49 +00:00
ed9b7edee3
Changed " to ' to stop the
...
[javadoc] /humgen/gsa-scr1/chartl/sting/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContext.java:99: warning: unmappable character for encoding ASCII
[javadoc] * if one of the alleles is deleted (?-?).
warnings on compile.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2703 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 15:23:55 +00:00
40c242d2b8
Fix for overflow issues
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2702 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 13:37:16 +00:00
8453676b71
added a method to AlignmentContext called hasExceededMaxPileup, which you can use to determine if the current site exceeded the maximum pileup size (reads were dropped). Added this as a check to unified genotyper according to Eric's instructions, and added the plumbing to the engine.
...
Also deleted the FixBamSortOrder package that isn't used anymore.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2701 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 05:17:01 +00:00
4bcdab580c
--output_dir has been changed to --output_prefix to give the user more control over the names of the resulting mass of files in AnalyzeAnnotations. The fontsize of the axes is increased. Cumulative filtering plots are removed since the binned filtering plots are much more useful.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2700 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 04:50:54 +00:00
df112e64b8
Minor tweaks
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2699 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 04:17:47 +00:00
476d6f3076
RealignerTargetCreator is officially live
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2697 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 03:41:52 +00:00
1f64c5d41a
Do not slurp the whole set of snp mask sites into memory (gets pretty heavy on full dbSNP!); instantiate a privare ROD iterator instead and drag it across the sites we are designing probes for.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2694 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 22:39:46 +00:00
47440bc029
- Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads.
...
- Reimplemented optimization in UG to not call when there are no non-ref bases.
- Compute reference confidence accurately in UG for ref calls.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2693 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 21:56:33 +00:00
2c8d7b0c44
Forgot the onTraversalDone. That was dumb.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2692 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 21:02:46 +00:00
04e1832968
Added - AlleleBalanceHistogramWalker -- hopefully this'll be able to tell us very clearly whether bad genotype concordance is a result of systematic contamination (consistent wonky allele balances)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2691 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 20:57:12 +00:00
a1054efe8a
Default platform and default read group are no longer set to values by default. The recalibrator throws an exception if needed values are empty in the bam file and the args weren't set by the user. This is done to make it more obvious to the user when the bam file is malformed. Similarly, the recalibrator now refuses to recalibrate any solid reads in which it can't find the color space information with an exception message explaining this. The recalibrator no longer maintains its own version number and instead uses the new global GATK version number.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2690 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 18:47:40 +00:00
0345d9f6a5
Updating the recalibrator to use non-depricated getPileup() method. Adding documentation to AnalyzeAnnotations so that the walker isn't marked as unclean at compile time.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2688 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 14:15:09 +00:00
c231547204
Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2687 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 13:53:29 +00:00
2e57bc7879
added a better message for the SO flag error in MergingSAMIterator2
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2685 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 22:57:18 +00:00
24d4082925
AnalyzeAnnotations can now process only variants that are found in samples that match the -sampleName argument. X-axis of plots no longer use annoying scientific notation.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2684 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 20:52:11 +00:00
022601b1a5
Warnings for walkers w/o Javadoc.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2683 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 20:34:50 +00:00
894a2b511b
Fixing no platform warning message.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2682 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 19:46:50 +00:00
2b51cf18f0
AnalyzeAnnotations now outputs plots with log x-axis in addition to standard x-axis so things like DP and MQ0 are easier to see. AnalyzeAnnotations now skips over all annotations that aren't floating point values. Recalibrator now warns users if PL tags are missing and so therefore it is reverting to illumina.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2681 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 19:39:18 +00:00
6cf413e630
Bug: ExpandedSAMRecord did not treat hard-clipped bases ('H') correctly. Fixed.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2680 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 19:23:44 +00:00
dc170caafc
Now, if a dbsnp rod is passed to either the UnifiedGenotyper or VariantAnnotator, a DB=0/1 annotation is added (in addition to filling in the ID field); this is in line with 1KG project calls. If no dbsnp rod is used, the annotation is not added (as opposed to setting every entry to DB=0).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2678 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 17:27:12 +00:00
5d2f8aaa54
Updating recalibrator version number after the several emergency changes last week.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2677 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 14:35:47 +00:00
588417e17d
Don't reference that optimiation library I'm not using anyway.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2676 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-24 20:30:50 +00:00
d3e3c1c2e0
don't require that optmization lib that I'm not using yet... (doh)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2675 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-24 20:28:21 +00:00
1d6d2b26f7
tools for optimizing calls.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2674 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-24 20:16:55 +00:00
877957761f
lots of new stuff, some generally useful, some one-off.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2673 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-24 19:50:48 +00:00
78890c0bee
First version of walker that combines the functionality of IndelIntervalWalker, MismatchIntervalWalker, SNPClusterWalker, and IntervalMergerWalker - plus it allows the user to input rods containing known indels (e.g. dbSNP or 1KG calls) for automatic cleaning. Basically, all pre-processing steps for cleaning are now done in a single pass.
...
More testing needed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2672 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-24 05:32:38 +00:00
d6b9b788a8
Renamed -- PlinkRodWithGenomeLoc --> PlinkRod
...
Since binary files do not need encoded locus information in the SNP names there's no need to suggest that it is so in the name of the rod
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2671 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 18:19:28 +00:00
ac983e7a0b
Ran the rod on a binary plink file with indels and it just worked. Love it when that happens! Unit test to ensure this behaviour is maintained.
...
****** PLINK ROD IS NOW READY TO GO ********
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2670 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 18:13:05 +00:00
ae22d35212
PlinkRod now correctly parses binary files without indels; unit test added for this behavior.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2669 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 17:34:06 +00:00
94dc09c865
PlinkRod now successfully instantiates on the binary ped file trio (.bim, .bam, .fam) for non-indel files.
...
Upcoming: Test that the instantiation is correct, do it for indel-containing files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2668 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 16:13:24 +00:00
01db93299c
PlinkRodWithGenomeLoc now properly handels indels.
...
There is now a DELETION_REFERENCE allele type to allow for the storage of multi-base references rather than point-mutation references.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2667 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 07:34:52 +00:00
42fb85e7f3
PlinkRodWithGenomeLoc now properly parses text plink files. Unit test added to test this functionality. Indels and binary files to come.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2666 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 06:19:26 +00:00
c871a0f221
UG map() now returns a VariantCallContext object. Also has a field for confidentlyCalledBases. UG reduce() emits statistics on the confident called % of bases
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2664 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 23:06:43 +00:00
fbf82526cb
Minor renamign changes.
...
PlinkRodWithGenomeLoc now supports .bed file parsing (and doesn't require |c#_p# conventions for SNPs -- still requires _g[I/D] for indels)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2663 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 23:06:32 +00:00
fd223e955c
Reverting the previous solid change. We now refuse to recalibrate if the solid read doesn't contain proper color space information. The exception message has been updated to say this. Also, Tile has been downgraded to an ExperimentalCovariate due to performance issues.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2662 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 20:55:28 +00:00
7732f98e56
Fix for Solid reads that have '.' in their color space field. The recalibrator will just set them to be illumina reads and won't apply color space correction.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2661 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 20:09:16 +00:00
2ea768d902
ant clean is your friend....fixed test code dependent on an interface change.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2660 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 20:07:46 +00:00
a11503819a
AnalyzeAnnotations now breaks out its TiTv plots into novel SNPs, dbSNP sites, and combined.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2659 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 19:00:23 +00:00
cc3b818268
cleanup of the pile-up limit exceeded warning, and a little code cleanup
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2657 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 22:17:24 +00:00
c1e09efb23
- Fixed output for beagle header
...
- Better description for QualByDepth annotation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2655 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 21:25:56 +00:00
d9df72e1b5
AnalyzeAnnotations now bins variants per each annotation and outputs plots of TiTv ratio as a function of the annotation's value.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2654 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 21:15:11 +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.
...
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.
...
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)
...
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.
...
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).
...
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.
...
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.
...
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.
...
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:
...
- 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
a1b4cc4baf
changes to intelligently log overflowing locus pile-ups.
...
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
...
- 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
ff66023d83
Trivial change to support filter field in VCF
...
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.
...
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
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
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
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
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
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
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
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
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
asivache
ebanks
rpoplin
hanna
depristo
chartl
aaron
jmaguire
kiran
mmelgar