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gatk3的最后一个经典版本3.8
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chartl 8d0e057d83 I got bored today and decided to write the confusion matrix calculator. At present it is untested. I'm submitting it to subversion to make sure 
I have  previous revision to revert back to.


This is a calculator that will calculate:

P[ True base is X | read base mismatches, secondary base is Y, previous K bases are Z1,Z2,...ZK ]

where the number of pervious reference bases to take into account is user-defined. The secondary base is optional as well.

--usePreviousBases k

tells the walker to use the k previous reference bases in the transition table

--useSecondaryBase

tells the walker to use the secondary base at a locus in the transition table

these can be used together.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1816 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-10-13 02:55:29 +00:00
R R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design. 2009-09-22 18:10:14 +00:00
c Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java I got bored today and decided to write the confusion matrix calculator. At present it is untested. I'm submitting it to subversion to make sure 2009-10-13 02:55:29 +00:00
packages moving IndelGenotyper out from playground 2009-09-25 19:43:53 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python simple monitor for watching pilot 1 call progress 2009-10-06 13:04:53 +00:00
scala/src support for scala walkers 2009-08-28 00:15:01 +00:00
settings epic fail! 2009-09-30 20:49:42 +00:00
shell Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one! 2009-09-04 12:39:06 +00:00
testdata GSA-182: Adding support for BED interval files. 2009-10-06 02:45:31 +00:00
build.xml changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script. 2009-09-10 04:31:33 +00:00
ivy.xml Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +00:00