gatk3的最后一个经典版本3.8

Menachem Fromer 6984ab0c78 Change ReadBackedPhasing to be VCF4.1 compliant (but instead of using PS tags, it uses HP tags for pairs of diploid haplotype labels). The important point is that it no longer uses the '|' character instead of '/' or flips around the allele order in the genotype. Instead, the HP FORMAT targ is used to mark the haplotype labels with respect to other genotypes for the same sample. Note that this enables the phasing of non-consecutive (but nearby) sites, based on mate pairs, for example. Also, updated the HaplotypeCallerValidation Qscript to perform PhaseByTransmission (if ped file given) and then ReadBackedPhasing		2013-01-08 16:40:32 -05:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	Bug fix in the HC's allele mapping for multi-allelic events. Using the allele alone as a key isn't sufficient because alleles change when the reference allele changes during VariantContextUtils.simpleMerge for multi-allelic events.	2013-01-07 11:05:44 -05:00
public	Change ReadBackedPhasing to be VCF4.1 compliant (but instead of using PS tags, it uses HP tags for pairs of diploid haplotype labels). The important point is that it no longer uses the '|' character instead of '/' or flips around the allele order in the genotype. Instead, the HP FORMAT targ is used to mark the haplotype labels with respect to other genotypes for the same sample. Note that this enables the phasing of non-consecutive (but nearby) sites, based on mate pairs, for example. Also, updated the HaplotypeCallerValidation Qscript to perform PhaseByTransmission (if ped file given) and then ReadBackedPhasing	2013-01-08 16:40:32 -05:00
settings	Final r119 tribble jar	2012-11-02 14:30:33 -04:00
.gitignore	adding some directories to gitignore	2012-09-27 11:09:41 -04:00
build.xml	Re-enabling contracts in tests in build.xml	2013-01-02 11:29:25 -05:00
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	Use build jars in test classpaths by default	2012-11-28 22:57:04 -05:00