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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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Eric Banks 841a906f21 Adding a hidden (for now) argument to UG (and HC) that tells the caller that the incoming samples are contaminated by N% and to fix it by aggressively down-sampling all alleles. This actually works. Yes, you read that right: given that we know what N is, we can make good calls on bams that have N% contamination. Only hooked up for SNPS right now. No tests added yet. 2012-10-20 23:31:56 -04:00
licensing Final final final version of the license. 2012-07-20 18:00:02 -04:00
protected/java Refactoring the Unified (and Standard) Argument Collections because it was really ugly that the subclass had to do all the cloning for the super class. The clone() method is really not recommended best practice in Java anyways, so I changed it so that we use standard overloaded constructors. Confirmed that the Haplotype Caller --help docs do not include UG-specific arguments. 2012-10-20 20:35:54 -04:00
public Adding a hidden (for now) argument to UG (and HC) that tells the caller that the incoming samples are contaminated by N% and to fix it by aggressively down-sampling all alleles. This actually works. Yes, you read that right: given that we know what N is, we can make good calls on bams that have N% contamination. Only hooked up for SNPS right now. No tests added yet. 2012-10-20 23:31:56 -04:00
settings Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component. 2012-10-16 02:22:30 -04:00
.gitignore adding some directories to gitignore 2012-09-27 11:09:41 -04:00
build.xml Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component. 2012-10-16 02:22:30 -04:00
intellij_example.tar.bz2 Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!) 2012-09-27 11:04:56 -04:00
ivy.xml Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component. 2012-10-16 02:22:30 -04:00