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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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hanna b0ec7fc144 More comprehensive testing of BWT (mismatches only) module, and lots of bug fixes. 
Limitations:
1) Can't handle RC alignments.
2) Can't handle indels.
3) Can't handle N's in reference bases.
4) Stops at first hit.

Ran BWT over a test suite of 800k Ecoli reads.  After removing alignments with indels / reads with Ns, the remaining reads were aligned with quality 'equal to' that of the alignment stored in the BAM file.  In this case 'equal' quality is <= mismatches to the reference as the existing alignment stored in the BAM file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1710 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-09-23 23:44:59 +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 More comprehensive testing of BWT (mismatches only) module, and lots of bug fixes. 2009-09-23 23:44:59 +00:00
packages Fail for missing resource files / scripts. 2009-09-22 21:31:01 +00:00
perl add wait id for 454 2009-09-22 01:41:58 +00:00
python Fixes for VariantEval for genotyping mode 2009-09-18 21:01:43 +00:00
scala/src support for scala walkers 2009-08-28 00:15:01 +00:00
settings Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +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 Framework for ROD walkers -- totally experiment and not working right now 2009-09-12 19:13:15 +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