Eric Banks 0b73573abc Slightly modifying the way to use the IUPAC ambiguity codes in the FastaAlternateReferenceMaker. ... Previously it required you to create a single sample VCF and then to pass that in to the tool, but Geraldine convinced me that this was a pain for users (because they usually have multi-sample VCFs). Instead now you can pass in a multi-sample VCF and specify which sample's genotypes should be used for the IUPAC encoding. Therefore the argument changed from '--useIUPAC' to '--use_IUPAC_sample NA12878'.		2014-04-02 21:34:25 -04:00
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src	Slightly modifying the way to use the IUPAC ambiguity codes in the FastaAlternateReferenceMaker.	2014-04-02 21:34:25 -04:00
pom.xml	Update pom versions to mark the start of GATK 3.2 development	2014-03-18 01:18:59 -04:00