Will see how this behaves for those using IntelliJ as generated source code will disappear during an ant clean.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4425 348d0f76-0448-11de-a6fe-93d51630548a
Why v3, you ask? Why not? Simply because v2 was a String so old and clunky, the sun would fizzle out and grow cold before any VCF could be successfully parsed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4421 348d0f76-0448-11de-a6fe-93d51630548a
1) Build the module with the following command:
$ ant gsalib
2) Add the module path to your ~/.Rprofile file:
.libPaths("/path/to/Sting/trunk/R/")
3) At the top of each R script that will use the library, include the line:
library(gsalib)
You can now use the package like any other R package. To get high-level documentation, supply the following command to R:
help(gsalib)
The methods contained herein are:
getargs : A method to easily provide arguments to interactive and non-interactive scripts.
Prints out a help message specifying how the script should be run if no arguments
or "-h" is provided. Very helpful when you're writing an R-script piecemeal in
interactive mode, then want to make it a command-line program.
plot.venn : Plots a two-way or three-way proportional Venn diagram.
read.eval : Reads VariantEval output that's formatted in R style.
read.gatkreport : Reads GATKReport output.
gsa.message : Emits a message with the prefix "[gsalib]" to stdout.
gsa.warn : Emits a warning message with the prefix "[gsalib] Warning:" to stdout.
gsa.error : Emits an error message with the prefix "[gsalib] Error: to stdout, calls traceback()
and halts execution.
Documentation on each of these methods can be obtained by typing "help(method_name)" at the R prompt.
* Retired GATKReport.R, as that functionality has now been moved to gsalib.
* Retired gsacommons, as that functionality has been split between gsalib and VariantReport.R.
* Modified VariantReport.R to make use of gsalib. The script now uses the getargs() method to provide the user with some information as to the proper way to run the script. Documentation on how to prepare output is given at http://www.broadinstitute.org/gsa/wiki/index.php/VariantEval .
* Added 'gsalib' target to build.xml file. Running "ant gsalib" will compile this module and place the R-ready package in R/gsalib .
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4416 348d0f76-0448-11de-a6fe-93d51630548a
Off to Yosemite in 4 hours, enjoy the week gsa folks!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4410 348d0f76-0448-11de-a6fe-93d51630548a
a) Fixed bugs in new dynamic programming-based genotyper
b) Fixed up temp hack that handles extended pileups for now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4398 348d0f76-0448-11de-a6fe-93d51630548a
- Brought over exact AF estimation from branch (which is now dead). Exact model is default in UnifiedGenotyperV2.
- Implemented completely new genotyping algorithm given best AF estimate using dynamic programming, which in theory should be better than both greedy search and any HWE-based genotyper.
- Integrated and added new Dindel likelihood estimation model.
- Corrected annotators that would call readBasePileup: since we can be annotating extended events, best way is to interrogate context for kind of pileup and either readBasePileup or readExtendedEventPileup.
All changes above except last one are still in playground since they require more testing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4396 348d0f76-0448-11de-a6fe-93d51630548a
where, when the system can't find a plugin of the correct name, the system
prefers to crap all over itself and throw an unintelligible NullPointerException
rather than displaying an intelligent error.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4393 348d0f76-0448-11de-a6fe-93d51630548a
the empty list. Score another victory for the integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4391 348d0f76-0448-11de-a6fe-93d51630548a
argument. Brought it back, and added an integrationtest to make sure it
stays around.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a
This will be librarized soon; but if you need to do something like this, feel free to cannibalize.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4387 348d0f76-0448-11de-a6fe-93d51630548a
ebanks
hanna
corin
kshakir
kiran
chartl
aaron
depristo
rpoplin
delangel
fromer