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gatk3的最后一个经典版本3.8
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kiran 62f5383859 * Added an R package, "gsalib", providing a place to store common, useful, documented R methods. To use this module, you must follow three steps: 
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
 		2010-10-04 00:27:59 +00:00
R * Added an R package, "gsalib", providing a place to store common, useful, documented R methods. To use this module, you must follow three steps: 2010-10-04 00:27:59 +00:00
archive Cleaning up playground utils and tests 2010-08-27 01:25:47 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also 2010-08-19 00:42:37 +00:00
java Fix typo and tell people not to post user errors 2010-10-03 18:58:03 +00:00
matlab Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function 2009-11-30 20:02:25 +00:00
packages Accidental fail to commit missing file. 2010-10-01 20:26:51 +00:00
perl Added 'Cron' to subject for easier message filtering 2010-09-28 21:03:50 +00:00
python clean-up the docs a little 2010-09-29 05:02:41 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Sigh. Fix the source of even more UserErrors in the phone home directory: make sure to gunzip the beagle files before passing them into the conversion walker... 2010-10-01 03:28:36 +00:00
settings The battle is over. Picard is revved. 2010-09-03 05:28:01 +00:00
shell Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00
testdata and add changes to the vcf used in testing 2010-06-25 02:56:02 +00:00
LICENSE Adding a license to the root directory in case BOSC checks for one. Has the 2010-04-20 16:04:29 +00:00
build.xml * Added an R package, "gsalib", providing a place to store common, useful, documented R methods. To use this module, you must follow three steps: 2010-10-04 00:27:59 +00:00
ivy.xml Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00