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Mark DePristo 1ee46e5c06 Collect only the bare essentials in the GATKRunReport 
Now looks like:
<GATK-run-report>
   <id>D7D31ULwTSxlAwnEOSmW6Z4PawXwMxEz</id>
   <start-time>2012/03/10 20.21.19</start-time>
   <end-time>2012/03/10 20.21.19</end-time>
   <run-time>0</run-time>
   <walker-name>CountReads</walker-name>
   <svn-version>1.4-483-g63ecdb2</svn-version>
   <total-memory>85000192</total-memory>
   <max-memory>129957888</max-memory>
   <user-name>depristo</user-name>
   <host-name>10.0.1.10</host-name>
   <java>Apple Inc.-1.6.0_26</java>
   <machine>Mac OS X-x86_64</machine>
   <iterations>105</iterations>
</GATK-run-report>

No longer capturing command line or directory information, to minimize people's concerns with phone home and privacy
 		2012-03-10 20:27:14 -05:00
..
R Now converts gatkreports to properly typed R data types in gsa.read.gatkreport 2012-03-02 09:11:59 -05:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles
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doc
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java Collect only the bare essentials in the GATKRunReport 2012-03-10 20:27:14 -05:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
perl Update to the bindings for liftOverVCF.pl (to -V from -B) 2011-09-15 15:33:09 -04:00
scala Mostly small changes to my own scala scripts: .vcf.gz compatibility for output files, smarter beagle generation, simple script to scatter-gather combine variants. Whole genome indel calling now uses the gold standard indel set. 2012-02-22 17:20:04 -05:00
testdata Added support for breakpoint alleles 2012-02-23 12:14:48 -05:00