c1263e841c
stop printing the debug info -- hurr
...
Also it turns out that sometimes there can be a call with zero total non-I/non-D bases -- so add one to numerator and denominator to prevent divide by zero error
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2262 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 16:17:38 +00:00
0c2d6d7e41
A brute-force script to convert Syzygy lod-score calls files into a proper VCF -- with some useful annotations.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2261 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 16:07:06 +00:00
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2260 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 14:56:48 +00:00
855face681
Histogram of covariate values now goes from 0 to max value which makes it look nicer in most cases.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2259 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 14:44:03 +00:00
985daec76e
Fixed problem with integer overflow in R scripts.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2258 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 14:24:49 +00:00
2508deca37
Prevented data points with fewer than N observations from going off the edge of the plots
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2257 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 13:55:43 +00:00
58937bf9ba
You can now use the -exp flag to tell the Genotyper to include experimental annotations when it calls out to VariantAnnotator.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2256 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 04:45:05 +00:00
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).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2255 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 04:04:39 +00:00
861221d046
- Moved various header line printing into a single method
...
- Fixed output for coverage above min depth
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2254 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 02:15:43 +00:00
2c7cb912f0
Bug fixes for mixed none/valued attributes. also now assigns fake float values for display, if requested, for covariates using the -plottable flag
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2253 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 23:52:35 +00:00
3eea1ece7a
Adding the ruby directory, and a simple script to restart Bamboo
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2251 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 22:48:48 +00:00
ac3895c218
Update the location of the DepthOfCoverage tool in the packaging system.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2250 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 19:11:53 +00:00
aef4be5610
Moved CoarseCoverageWalker to core and packaged both coverage walkers in coverage/
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2249 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:53:36 +00:00
df4e001a07
Renamed to more accurately describe its function.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2248 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:34:49 +00:00
c2017cc91b
PrintCoverageWalker functionality moved to DepthOfCoverageWalker. Added integration tests.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2247 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:23:59 +00:00
608fa4cc3a
Update packaging system to produce multiple jars if asked nicely.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2246 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:11:12 +00:00
01cf5cc741
1. Merged CoverageHistogram into DepthOfCoverageWalker
...
2. Fixed bug in histogram calculation for small intervals
3. Better output in DoCWalker
4. Comments added to code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2245 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:01:53 +00:00
44b9f60735
PercentOfBasesCovered functionality moved to DepthOfCoverageWalker. Added integration tests.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2244 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 16:11:09 +00:00
126d1eca35
Move to core (qc/)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2243 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 15:45:58 +00:00
9da5cc25ad
More archiving (with permission from Andrey) plus a move to core.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2242 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 15:40:27 +00:00
b3bdcd0e60
make sure we close the error log stream in CommandLineProgram if it's opened; unit tests and clean-up for BasicVariation
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2241 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 06:59:27 +00:00
d27d56ea0c
adding the option to not halt after a test failure; it will still report failure at the end. This makes sense for Bamboo so we know all the tests that fail, not just the first. It is also useful for checking what tests are affected by a change.
...
You can tell ant not to halt with: 'ant -Dhalt=no' (yes is the default)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2240 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 06:19:39 +00:00
a88202c3f6
Refactored DoCWalker to output in a more helpful and usable style. It now outputs in tabular format with 2 different sections: per locus and then per interval.
...
I am now at a point where I can merge the functionality from other coverage walkers into this one.
Thanks to Andrew for input.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2239 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 05:28:21 +00:00
d7e4cd4c82
Moving some useful and stable walkers to core:
...
- ClipReads
- PrintRODs (generalized to print all RODs that are Variations)
- FixBAMSortOrderTag (added documentation to walker so that people know what it does and why)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2238 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 03:00:45 +00:00
2460f2a789
minor update to build.xml for CG utilities. Hopefully bamboo will be back online
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2237 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 00:06:02 +00:00
0b6b92bf5b
Fix (hopefully) the rest of the problems with the build.xml svn merge.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2236 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:53:31 +00:00
f41965a73e
Fixed incompatiblity in variable name between my script and the new elements merged into my script.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2235 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:40:50 +00:00
357abc9e89
Update build.xml to make it oneoffprojects-aware, and do some misc formatting cleanup and moves.
...
Here goes nothing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2234 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:27:45 +00:00
46f3d3e39b
Added comments to AnalyzeCovariates and R scripts. R script prevents residuals from going off the edge of the plot. Added skeleton code to the recalibration walkers showing how we plan to handle SOLID reference inserting behavior.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2233 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:15:52 +00:00
451a20ed55
commenting out some broken integration tests, to be uncommented if needed.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2232 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:13:24 +00:00
dbb8b86ed1
Minor updates to correctly handle emitting FN calls
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2231 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 22:53:17 +00:00
c776f9fb90
Simple utilities for dealing with Complete Genomics data
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2230 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 22:51:41 +00:00
9d598f1c82
some integration test clean-up
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2229 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 21:11:02 +00:00
a09fee2b5e
Moved some more walkers to oneoffprojects and killed an old indel-related walker that isn't being used.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2228 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:28:07 +00:00
dec0a781c2
Un-reinventing the wheel. --sleep argument removed.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2227 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:19:28 +00:00
938017d887
Removed ReadQualityRecalibrator.xml
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2226 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:14:14 +00:00
a3343c75db
Move and rename a hybrid-selection-specific coverage calculation to hybridselection/
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2225 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:11:22 +00:00
2c83f2f2bc
Move MSG - plus now obsolete classes which it depends on -- to oneoffprojects (with permission from Jared).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2224 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:04:22 +00:00
9c597309d3
Changed the sizes of the dots and bars on the plots generated by the R script which is called from AnalyzeCovariates.java
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2223 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 19:47:48 +00:00
93842abb4a
Let the packages know about the changes made for AnalyzeCovariates.jar
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2222 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 19:09:53 +00:00
c524b8e84b
add VCFTool.jar
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2221 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 19:04:38 +00:00
6a9e7bea05
Removing experimental annotations
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2220 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 19:03:55 +00:00
c180a76b05
Added option "append": if set, and the specified discovery output already exists, don't re-call anything that's already present in that file. Append new calls to it.
...
Great for resuming long jobs that died partway through.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2219 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 18:56:19 +00:00
0a2304eff8
- Rename minConfidenceScore in VariantEval to minPhredConfidenceScore
...
- Moved validation walkers to new qc dir
- Killed unused test
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2218 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 17:59:19 +00:00
a5dfc9107d
- Cleaned up annotation code some more
...
- Use QualityUtils when phred-scaling now
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2217 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 17:45:29 +00:00
7055a3ea2d
- All annotations are now required to return their VCF INFO keys and descriptions
...
- Renamed keys to fit with the standard naming
- FisherStrand is no longer standard
- Integration tests no longer test experimental annotations since they're not stable
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2216 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 17:24:06 +00:00
67179e2412
Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2215 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 16:47:35 +00:00
2838629724
-VCF writer now checks whether the allele frequency has been set before trying to write it out.
...
-Renamed methods to be more consistent.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2214 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 16:25:32 +00:00
6231637615
fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2213 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 15:41:35 +00:00
8a87d5add1
misc. bug fixes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2212 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 14:36:03 +00:00
chartl
ebanks
rpoplin
depristo
aaron
hanna
jmaguire