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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%
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ebanks 98f7679619 Fixed the bug reported on GS regarding a clipped read that got moved several hundred bases away. The code that got triggered here was written back in the original version of the cleaner and it never actually did the right thing. 
While I was fixing it, I noticed that we weren't allowing the cleaner to un-clean reads with indels when they're wrong even though we should.  Hypothetically, that should rarely happen: only when we can left-align out an indel or when the original mapper really went haywire.  This situation is rare enough that I'm calling logger.info to let the user know it's happening and suggesting that they double-check that everything looks right with their reads.  Better to be extra-cautious now that the cleaner is moving into the 1kg and Broad production pipelines soon
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Mark, have no fear: this was truly a rare edge case - one that won't affect the cleaning stats.  There is no need to re-clean the data processing paper bams!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4057 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-19 01:42:48 +00:00
R Nicer plotting routine for tranches. Add a third arg to suppress the legend. 2010-08-17 19:20:58 +00:00
archive Archiving 2010-07-27 02:47:18 +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 Fixed the bug reported on GS regarding a clipped read that got moved several hundred bases away. The code that got triggered here was written back in the original version of the cleaner and it never actually did the right thing. 2010-08-19 01:42:48 +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 Enabling support for any scala used in QScripts. 2010-08-17 22:05:56 +00:00
perl Change for Chris: don't depend on other Perl modules. 2010-08-17 22:19:13 +00:00
python now support -o output option, useful for pipelines 2010-08-06 14:57:04 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala 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
settings 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
shell Useful script to see the status of gsa computing resources. Crontab'd and will be arriving as email at 8 am 2010-08-07 12:36:28 +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 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
ivy.xml 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