zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
2,756 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

2321 Commits (f7e7bcd2efa6eb5cbf87913e336f09b64bc1c0ac)

Author SHA1 Message Date
depristo 9876645a5d Now drives the walker by reference, not by reads, so we see even loci with no reads. This allows us to accurately calculate the true total callable area 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2720 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 11:12:46 +00:00
ebanks 1dd9996f3a New realigner now completely uses bytes, plus misc fixes. Still not ready for use. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2719 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 04:17:20 +00:00
depristo f6bca7873c V3 of VariantContext. Support for Genotypes and NO_CALL alleles. QUAL fields fully implemented. Can parse VCF records and dbSNP. More complete validation. Detailed testing routines for VariantContext and Allele. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2718 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 04:10:16 +00:00
chartl 23fc9737b4 Added the ability to filter out variant (not truth) calls based on read depth. Using -NLD 5 will not update concordant counts for calls with 0, 1, 2, 3, or 4 reads supporting them. Not to be used with VCF files that do not have DP in the format field. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2716 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 23:28:04 +00:00
chartl 1b9184a1c7 Added a multisample concordance walker which takes the place of the VCF python library I've been using. Takes a truth VCF and a variant VCF and outputs A TSV that looks like this: 
Sample_ID       Concordant_Refs Concordant_Vars Homs_called_het Het_called_homs False_Positives False_Negatives_Due_To_Ref_Call False_Negatives_Due_To_No_Call
NA19381 491     294     2       0       0       0       1
NA19451 489     298     1       0       0       0       0
NA19463 486     289     2       3       1       4       3
NA19376 488     296     1       0       2       0       1
NA19317 489     284     5       3       3       3       1


This walker will be merged with GenotypeConcordance once it's clear how to do so. 



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2715 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 22:59:17 +00:00
asivache 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
ebanks 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
rpoplin 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
rpoplin 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
rpoplin 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
hanna 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
depristo 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
asivache 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
chartl 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
depristo 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
aaron 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
rpoplin 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
chartl 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
ebanks 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
asivache 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
ebanks 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
chartl 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
chartl 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
rpoplin 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
rpoplin 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
depristo 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
aaron 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
rpoplin 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
hanna 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
rpoplin 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
rpoplin 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
asivache 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
ebanks 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
rpoplin 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
jmaguire 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
jmaguire 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
jmaguire 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
jmaguire 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
ebanks 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
chartl 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
chartl 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
chartl 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
chartl 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
chartl 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
chartl 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
depristo 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
chartl 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
rpoplin 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
rpoplin 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
aaron 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
rpoplin 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
aaron 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
ebanks 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
rpoplin 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
chartl 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
chartl 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
asivache 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
hanna 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
ebanks 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
hanna 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
aaron 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
hanna 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
chartl 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
aaron 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
ebanks 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
depristo 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
asivache 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
hanna 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
depristo 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
rpoplin 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
chartl 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
hanna 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
rpoplin 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
rpoplin 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
rpoplin 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
rpoplin 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
kiran 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
kiran 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
ebanks 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
ebanks 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
depristo 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
depristo 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
depristo 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
depristo 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
depristo 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
hanna 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
hanna 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
rpoplin 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
hanna 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
mmelgar 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
asivache 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
asivache 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
asivache 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
asivache 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
rpoplin 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
rpoplin 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
ebanks 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
rpoplin 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
asivache 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
rpoplin 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