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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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asivache 52eedaf22d Subtle but very annoying bug due to incorrect exit condition on backward traversal. Example of incorrect old behavior (found by Martha Borkan, this normally would NOT happen with the combination of match/mismatch/open/extend parameters we have been using; use match=10.0, mismatch= -9.0, open= -15.0, extend= -6.66 in older builds in order to reproduce): 
let's align two sequences (shown below, good alignment)

AAATTTGGTAAAA-GT
AAATTTGGTAAAAGGT

now let's reverse the same very sequences and align again

 TGAAAATGGTTTAAA
TGGAAAATGGTTTAAA

Note how we lost the deletion and got a mismatch instead at the very first letter of the upper sequence. The overall score of any particular alignment does not depend on the direction of the traversal, so the best alignment (with the highest score) should stay the same too.

New version fixes this issue and produces correct alignment of reverse sequences (up to the different choice of redundant position for the deletion):

T-GAAAATGGTTTAAA
TGGAAAATGGTTTAAA

This version also has the main() method reinstated, so the aligner can be run on its own as a little app.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5255 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-02-17 00:02:32 +00:00
R Now says FNR, not FDR. We really need to clean up VQSR 2011-02-15 12:28:09 +00:00
analysis/depristo Scripts to create the GATK IAM user and give him/her rights to PutObject (and only PutObject) into the S3 storage instance. Updated the GATKRunReport to now upload using the GATK user, not mark@depristo.com. Running with -et AWS_S3 sends run reports up to the Amazon S3 cloud now. Going to request a few external users try this option so we can see it running at scale. I'm sure S3 can handle a few hundred thousand 1Kb uploads per days, though 2011-01-31 03:48:33 +00:00
archive Moving GLF code to archive 2011-01-15 22:42:42 +00:00
c Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base. 2010-12-17 14:49:15 +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 Subtle but very annoying bug due to incorrect exit condition on backward traversal. Example of incorrect old behavior (found by Martha Borkan, this normally would NOT happen with the combination of match/mismatch/open/extend parameters we have been using; use match=10.0, mismatch= -9.0, open= -15.0, extend= -6.66 in older builds in order to reproduce): 2011-02-17 00:02:32 +00:00
lua forgot to remove a debug line. 2011-02-15 16:25:48 +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 Adding the native jna support libraries from the jna.jar to the Queue package jar. 2011-01-08 10:48:30 +00:00
perl Fixed bug that required users to use the recordOriginalLocation option 2011-01-05 23:12:14 +00:00
python Modifications, bugfix to theoretical posteriors. (Bug fix: eliminated discontinuity in prior distribution) 2011-02-14 19:47:34 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Data Processing Pipeline: local indel realignment, mark duplicates and BQSR. Done. 2011-02-16 17:22:30 +00:00
settings Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
shell Slightly better output now -- no longer emitting pdfs by default. Emails will go to gsamembers now 2011-02-10 13:02:24 +00:00
testdata VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary 2010-11-15 22:19:22 +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 A few more unit tests plus some extra 2011-02-09 01:51:34 +00:00
ivy.xml Added commons math, for Kristian. 2011-02-14 18:57:21 +00:00