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  • 1389ac6bdf Hurrr -- this uses power as part of its output. Changes to the power calculation broke the md5s RIGHT AFTER I HAD FIXED THEM arghflrg. chartl 2009-12-14 22:42:50 +0000
  • b42fc905e8 Added - new tests (Hapmap was re-added) chartl 2009-12-14 21:57:20 +0000
  • 8e44bfd2ef CycleCovariate and PrimerRoundCovariate now correctly handle negative strand 454 and SOLID reads. rpoplin 2009-12-14 21:52:30 +0000
  • c7b23d6ca5 Now that VCFGenotypeRecords implement SampleBacked (as they should), a quick fix was needed to get the GenotypeConcordance working when no direct samples were provided in a samples file. ebanks 2009-12-14 04:27:16 +0000
  • bd7b07f3f1 added PrimitivePair.Long and a few shortcut utility methods to PrimitivePairs: add(pair), subtract(pair), assignFrom(pair) asivache 2009-12-14 00:15:44 +0000
  • 97618663ef Refactored and generalized the VCF header info code. ebanks 2009-12-13 21:02:45 +0000
  • 05b8782d5f Documentation updates. Moved CountX.java walkers to QC depristo 2009-12-13 18:40:22 +0000
  • 92307361a4 In preparation for move depristo 2009-12-13 18:28:06 +0000
  • 56467df49a minor improvements to snpSelector to work with hapmap chip VCF files depristo 2009-12-13 17:59:32 +0000
  • 45199136f0 Completed my documentation responsibilities - based on Mark's reasonable assignment and not the one Matt made up while on Meth. ebanks 2009-12-13 04:13:30 +0000
  • bd2a46ab4c I want to move over to hpprojects tonight, so I'm checking in various changes all in one go: 1. Initial code for annotating calls with the base mismatch rate within a reference window (still needs analysis). 2. Move error checking code from rodVCF to VCFRecord. 3. More improvements to SNP Genotype callset concordance. 4. Fixed some comments in Variation/Genotype ebanks 2009-12-13 02:52:18 +0000
  • 2748eb60e1 Added short documentation for each class so that it appears in the walker command-line documentation. kiran 2009-12-12 21:41:07 +0000
  • 78e94b5a84 TableRecalibration now puts the full list of walker arguments into the PG tag of the bam file it creates. Thanks Matt and Eric. Also, the default nback for the HomopolymerCovariate is 8, down from 10. rpoplin 2009-12-12 17:29:41 +0000
  • 014013630f Added hieracrchy to the covariate classes: Required, Standard, and Experimental. Required covariates (rg and reported quality) are added for the user whether or not they are specified in the -cov list. There is now a -standard option in CountCovariates which will add in all of the standard covariates so the user doesn't have to type them all out or even know which ones are the standard. There is logger output to say which covariates are being used of course. The list of covariates used is also added to the PG tag in the bam file produced by TableRecalibration. rpoplin 2009-12-12 16:34:05 +0000
  • 6955b5bf53 Cleanup of the doc system, and introduce Kiran's concept of a detailed summary below the specific command-line arguments for the walker. Also introduced @help.summary to override summary descriptions if required. hanna 2009-12-12 04:04:37 +0000
  • cdfe204d19 Incorporated feedback from Kiran. Use the Javadoc first sentence extraction capability to just show the first sentence from each line of Javadoc. @help.description can still be used to produce exceptionally verbose descriptions. Also increased the line width as much as I could tolerate (100 characters -> 120 characters). hanna 2009-12-11 21:59:55 +0000
  • 4fa4e95fbc Updated AnalyzeCovariates to extend org.broadinstitute.sting.utils.cmdLine.CommandLineProgram and use the standard argument parsing. rpoplin 2009-12-11 21:57:18 +0000
  • 38d9f7b903 Renamed ReferenceContext's getSimpleBase() method to getBaseIndex() kiran 2009-12-11 20:14:39 +0000
  • 09811b9f34 Now that we always output the VCF header, make sure that we correctly handle the situation where there are no records in the file. Added unit tests as well. aaron 2009-12-11 19:51:05 +0000
  • 0da2105e3c Moving DuplicateQualsWalker to oneoffprojects. hanna 2009-12-11 19:22:32 +0000
  • 60c3eb4b60 Added help.description to the recalibration walkers. rpoplin 2009-12-11 19:02:29 +0000
  • 2ea7632b76 The SNP genotype concordance module is now more comprehensive. ebanks 2009-12-11 18:34:33 +0000
  • 590aeee7d2 Documentation for more basic walkers. hanna 2009-12-11 18:15:40 +0000
  • d1815f3559 More documentation for walkers that I'm familiar with in the collection of core walkers. hanna 2009-12-11 18:02:33 +0000
  • 956c36a2c8 Help for the qc package. hanna 2009-12-11 17:32:47 +0000
  • 450ea233a5 Docs for the basic walkers: CountLoci, CountReads. hanna 2009-12-11 17:17:34 +0000
  • f97ac939fa Punch up the help documentation for CombineDuplicates. hanna 2009-12-11 17:09:35 +0000
  • 86dc98bfb5 update the documentation for CombineDuplicates for the new help system. aaron 2009-12-11 17:01:42 +0000
  • 420725441a documentation updates for the new help system. aaron 2009-12-11 16:15:44 +0000
  • 23d96b1d43 Help system content for the alignment module. hanna 2009-12-11 16:01:25 +0000
  • 2de7e1a178 Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample. The only major difference is that we are now able to get accurate allele balance ratios. ebanks 2009-12-11 05:28:28 +0000
  • 8f7554d44f A few improvements to pooled concordance calcluations. Now will show you FN with the -V option. BasicGenotype now prints out a reasonable representaiton wiwth toString depristo 2009-12-10 23:09:10 +0000
  • f64a4c66ac some tweaks for the GATK paper genotyper to better work with shared memory parallelization, added documentation changes for Matt's new help system. aaron 2009-12-10 22:33:51 +0000
  • a7cd172628 Added 8x coverage field and minimum base quality command line option in order to be able to compare to U. Wash. exome metrics. andrewk 2009-12-10 22:14:44 +0000
  • 1ae333a1c1 R script for graphing depth of coverage by sample name, and generating a loess curve for each sample's data. aaron 2009-12-10 21:58:01 +0000
  • 088363ce42 Added entropy calculation to histogram of quality scores rpoplin 2009-12-10 21:57:35 +0000
  • 2869270c11 Fixed deletion depth calculation plus mis-spelling in ReadBackedPileup method. ebanks 2009-12-10 21:11:42 +0000
  • 31b1d60d28 Generalized the StratifiedAlignmentContext code so that it's easy to add new ways to stratify. Then added an MQ0-free stratification so we don't need to be carrying around 2 different alignment contexts (full vs. mq0-free) anymore. ebanks 2009-12-10 19:50:06 +0000
  • 0c396f04a2 Fix obvious cut/paste error in output stream management code. hanna 2009-12-10 19:23:13 +0000
  • 11ac7885b0 Pull out StratifiedAlignmentContext code so other walkers can use it. This is basically a wrapper class around AlignmentContext which allows you to stratify a context by e.g. reads on forward vs. reverse strands. ebanks 2009-12-10 19:21:16 +0000
  • adb2fdbee7 Before, we were only checking that the reference was present if @Requires required that a reference was present. Now we always check that a reference is present, so that we get an intelligent error message. hanna 2009-12-10 19:15:48 +0000
  • 5eac510b2f Refactor the code I gave Eric yesterday to output command line arguments. Convert it from a completely wonky solution to a slightly less wonky solution that will work in more cases. hanna 2009-12-10 18:57:54 +0000
  • 74b8055b6a Only show extra walker help if the user didn't specify a walker or specified an invalid walker. hanna 2009-12-10 16:43:06 +0000
  • e6f541fdca Forgot to update integration test last night ebanks 2009-12-10 12:57:10 +0000
  • b2dfe85648 Better support for reading truth file depristo 2009-12-10 12:16:05 +0000
  • 0fae798b3a 1. Discoverable base calculations don't care about Genotypes (use Variation's PError regardless of whether the call is ref or var - it's the correct value even for ref calls). 2. Call a base genotypable if any of the Genotypes is above the threshold (you can't assume there's a single Genotype associated with the Variation). ebanks 2009-12-10 04:26:06 +0000
  • a45adadf1f VCFGenotypeRecord already defines all the methods needed to be SampleBacked, so let's annotate it as being SampleBacked. This way, when used as a generic Genotype, sample data can be retrieved. ebanks 2009-12-10 04:16:21 +0000
  • 78d5ac9bc2 Don't check het count when there are multiple Genotypes per Variation. ebanks 2009-12-10 04:07:47 +0000
  • ee691b8899 Added a whole bunch of unit tests for VCF reading. We could still use more, but this is a good start. ebanks 2009-12-10 03:31:23 +0000
  • 6a4118ad3c grr, ought to actually assign it to the TRUTH_CALLS variable chartl 2009-12-09 23:31:46 +0000
  • 987fced151 Should read truth data from the parser options rather than direct from args chartl 2009-12-09 23:26:26 +0000
  • f7c44ad019 - Read in arguments for the header based on reflection - Hook up Variation and Genotype in SSG ebanks 2009-12-09 21:35:33 +0000
  • 8825211fdb Adding this to subversion so it's protected chartl 2009-12-09 21:26:17 +0000
  • 12ec154f01 Make the AnalyzeCovariate plots look a little nicer when there are a small number of data points rpoplin 2009-12-09 21:22:40 +0000
  • 408f6f3dee Refactoring of prior commit: better handling of unnamed package within the help system. hanna 2009-12-09 20:12:35 +0000
  • 1d2151adcf Better handling of nulls output by hanna 2009-12-09 19:34:56 +0000
  • 40c2d7a4bc Fix all-bases-mode and genotype-mode in the UG and add integration tests for them. ebanks 2009-12-09 17:41:30 +0000
  • 4e54b91ce4 UG now outputs the FORMAT header fields when there's genotype data. ebanks 2009-12-09 16:31:07 +0000
  • 12c49ea485 Added DuplicateReadFilter to filter out reads that are marked as duplicates. rpoplin 2009-12-09 15:42:53 +0000
  • fb900b12e1 VariantFiltration now details the filters it has used in the header of the VCF it produces. ebanks 2009-12-09 15:36:15 +0000
  • 7a76e13459 Better explanation in the exception being thrown. ebanks 2009-12-09 03:59:36 +0000
  • 8d67d9ade3 -Minor fix in UG for all-bases mode -Make minConfidenceScore in VariantEval a double so non-integer values can be used (requested by Steve H). ebanks 2009-12-09 03:49:10 +0000
  • 8a1c876104 Weird. I thought I had updated these md5s... ebanks 2009-12-09 03:31:41 +0000
  • 717eb1de96 - Depth annotation now includes MQ0 reads - Removed MQ0 annotation - Updated RMS MQ annotation to use new pileup - UG now outputs all of its arguments as key/value pairs in the header (for VCF) - Cleaned up VCFGenotypeWriterAdapter interface a bit ebanks 2009-12-09 02:53:00 +0000
  • e8822a3fb4 Stage 3 of Variation refactoring: We are now VCF3.3 compliant. (Only a few more stages left. Sigh.) ebanks 2009-12-08 21:43:28 +0000
  • 9e2f831206 A bit of cleanup in preparation for Picard patch. hanna 2009-12-08 16:09:04 +0000
  • d3b78338da Get rid of characters in the docs that aren't universally compatible with character sets used throughout the group. hanna 2009-12-07 21:41:07 +0000
  • d75d3a361a Clean up some of the walker help output based on additional experience and feedback received. Also, add a flag to build.xml to disable generation of docs on demand (use ant -Ddisable.doc=true to disable docs). hanna 2009-12-07 21:33:11 +0000
  • 2cf21317f9 Create package that contains just what Picard needs. alecw 2009-12-07 21:22:07 +0000
  • a3e88c0b1c Cleanup results of bad merge. hanna 2009-12-07 19:30:49 +0000
  • 10be5a5de9 Move some files around to reflect our growing help infrastructure. hanna 2009-12-07 19:23:12 +0000
  • 16ef500139 Tweak the build.sysclasspath option to force the system classpath to always be appended to additional jars added to the classpath by us. These seemed to be set differently depending on the platform or distribution before. hanna 2009-12-07 19:19:29 +0000
  • c9e385f541 Add TileCovariate to GenomeAnalysisTK package alecw 2009-12-07 16:39:59 +0000
  • 1d5b9883db Added --solid_recal_mode argument to experiment with different ways of dealing with solid reference bias. Currently the default option is DO_NOTHING which means use the same behavior as the old recalibrator. Eventually the new methods in RecalDataManager will be moved over to a SolidUtils class. Added transition and transversion methods to BaseUtils that work like simpleComplement, used with the color space in my solid methods. Also, initial check-in of HomopolymerCovariate. rpoplin 2009-12-07 14:26:27 +0000
  • 2632cb6b58 minor improvements to snp selector depristo 2009-12-07 03:37:14 +0000
  • 8f461d3c40 Critical bug fix for VariantEval dbSNP calculations. Moved the system over to the new improved ROD iterators, resulting in dbSNP rates jumping 5% or so, due to masking of true SNPs by preceding indels. depristo 2009-12-07 03:36:38 +0000
  • 8089aa3c50 Adding support to override the help text. hanna 2009-12-07 00:16:26 +0000
  • c0528cd88e Updated the CallsetConcordance classes to use new VCF Variation code... and uncovered a whole bunch of VCF bugs in the process. I'm not convinced that I got them all, so I'll unit test like crazy when the refactoring is done. ebanks 2009-12-06 11:43:40 +0000
  • b6f8e33f4c Stage 2 of Variation refactoring: VCFRecord now implements Variation, VCFGenotypeRecord now implements Genotype. ebanks 2009-12-06 06:48:03 +0000
  • 3b440e0dbc Add a taglet to allow users to override the display name in command-line help. hanna 2009-12-06 04:12:10 +0000
  • 08f2214f14 Stage 1 of massive Variation/Genotype refactoring. ebanks 2009-12-06 03:12:41 +0000
  • b817db0962 Syzygy has a default LOD score of 0.91 on bases with no coverage, this is problematic. Set the minimum lod threshold to 1 because I just don't want to see that codswallop. chartl 2009-12-04 23:29:14 +0000
  • b04de77952 First pass at a reorganized walker info display. Groups walkers by package and displays walker data extracted from the JavaDoc. Needs a bit of help, both in content and flexibility of package naming. hanna 2009-12-04 23:24:29 +0000
  • 07b88621c5 Improved RankSum calculations and RankSum annotation. Much more meaningful depristo 2009-12-04 22:16:40 +0000
  • 0753315156 updates to the python snp selector -- now sorts info fields and we stop printing unnecessary debugging info in vcf2table depristo 2009-12-04 22:16:02 +0000
  • 0f89a38473 forgot to commit this earlier chartl 2009-12-04 22:10:16 +0000
  • 4c147329a9 Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file in GenomeAnalysisTK.jar. Still no support for actually displaying the archived javadoc. Also change the approach to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java. hanna 2009-12-04 20:08:41 +0000
  • c1263e841c stop printing the debug info -- hurr chartl 2009-12-04 16:17:38 +0000
  • 0c2d6d7e41 A brute-force script to convert Syzygy lod-score calls files into a proper VCF -- with some useful annotations. chartl 2009-12-04 16:07:06 +0000
  • 1e8dcc30da -dbSNP rod should not implement VariantBackedByGenotype since dbsnp records have no genotype data -added code to cache the allele list so it didn't need to get recomputed each time it was requested. ebanks 2009-12-04 14:56:48 +0000
  • 855face681 Histogram of covariate values now goes from 0 to max value which makes it look nicer in most cases. rpoplin 2009-12-04 14:44:03 +0000
  • 985daec76e Fixed problem with integer overflow in R scripts. rpoplin 2009-12-04 14:24:49 +0000
  • 2508deca37 Prevented data points with fewer than N observations from going off the edge of the plots rpoplin 2009-12-04 13:55:43 +0000
  • 58937bf9ba You can now use the -exp flag to tell the Genotyper to include experimental annotations when it calls out to VariantAnnotator. ebanks 2009-12-04 04:45:05 +0000
  • b05e73a914 Finished implementation of the Wilcoxon Rank Sum Test thanks to Tim Fennell (calculating the normal approximation) and Nick Patterson (dithering to break tie bands). ebanks 2009-12-04 04:04:39 +0000
  • 861221d046 - Moved various header line printing into a single method - Fixed output for coverage above min depth ebanks 2009-12-04 02:15:43 +0000
  • 2c7cb912f0 Bug fixes for mixed none/valued attributes. also now assigns fake float values for display, if requested, for covariates using the -plottable flag depristo 2009-12-03 23:52:35 +0000
  • 3eea1ece7a Adding the ruby directory, and a simple script to restart Bamboo aaron 2009-12-03 22:48:48 +0000
  • ac3895c218 Update the location of the DepthOfCoverage tool in the packaging system. hanna 2009-12-03 19:11:53 +0000
  • aef4be5610 Moved CoarseCoverageWalker to core and packaged both coverage walkers in coverage/ ebanks 2009-12-03 17:53:36 +0000