gatk3的最后一个经典版本3.8

David Roazen e1cb5f6459 SnpEff annotator now assigns a functional class to each effect and distinguishes between actual effects and mere modifiers. ... -We now assign a functional class (nonsense, missense, silent, or none) to each SnpEff effect, and add a SNPEFF_FUNCTIONAL_CLASS annotation to the INFO field of the output VCF. -Effects are now prioritized according to both biological impact and functional class, instead of impact only. -Many of SnpEff's "low-impact" effects are now classified as "modifiers" with lower priority than every other effect. This includes such "effects" as DOWNSTREAM, UPSTREAM, INTRON, GENE, EXON, and others that really describe the location of the variant rather than its biological effect. This code will be short-lived (likely 1.2-only), as the next version of SnpEff will include most of these features directly. Checking this change into Stable+Unstable instead of Unstable because the current functional class stratification in VariantEval is basically broken and urgently needs to be fixed for production purposes.		2011-09-23 16:06:52 -04:00
public	SnpEff annotator now assigns a functional class to each effect and distinguishes between actual effects and mere modifiers.	2011-09-23 16:06:52 -04:00
settings	Revving the Tribble jar where the DbsnpCodec class was renamed to OldDbsnpCodec. Updating GATK code accordingly.	2011-09-06 20:39:42 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	To work around potential problem with invalid javax.mail 1.4.1 in ivy cache, added explicit javax.mail 1.4.4 along with build.xml code to remove 1.4.1.	2011-09-20 00:14:35 -04:00
ivy.xml	To work around potential problem with invalid javax.mail 1.4.1 in ivy cache, added explicit javax.mail 1.4.4 along with build.xml code to remove 1.4.1.	2011-09-20 00:14:35 -04:00