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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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VectorPairHMM Removed g_haplotype* global variables in native code so that it works 2014-03-06 22:08:35 -08:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
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doc Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
external-example Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
gatk-framework Slightly modifying the way to use the IUPAC ambiguity codes in the FastaAlternateReferenceMaker. 2014-04-02 21:34:25 -04:00
gatk-package Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
gatk-queue-extgen Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
gsalib Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
java/config Moved files to maven directories. 2014-02-03 13:50:44 -05:00
package-tests Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
queue-package Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
repo Rev Picard 1.110.1773 2014-03-31 14:15:06 -04:00
sting-root Rev Picard 1.110.1773 2014-03-31 14:15:06 -04:00
sting-utils Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
pom.xml Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00