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Phillip Dexheimer 6190d660e0 Edits to work with the latest htsjdk release: 
* TextCigarCodec.decode() is now static, and the getSingleton() method is gone
 * MergingSamRecordIterator now wants a Collection<SamReader> rather than Collection<SAMFileReader> in the constructor
 * SeekableBufferedStream now correctly reads the requested number of bytes, removed workaround in GATKBAMIndex
 		2015-01-13 21:32:10 -05:00
..
VectorPairHMM Do not use logger, write to stderr, could not get the correct logger dependency in pom.xml 2015-01-06 10:32:11 -05:00
c After renaming the packages, instead of updating the JNI library used for testing bwa, moving the classes to the archive. 2014-05-19 17:36:41 -04:00
chainFiles The contig is named MT not M in b36. Delivers PT68890442. 2014-04-08 10:03:47 -04:00
doc Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
external-example Faster builds, with updates to documentation generation. 2014-11-05 00:32:23 +08:00
gatk-engine Edits to work with the latest htsjdk release: 2015-01-13 21:32:10 -05:00
gatk-queue Faster builds, with updates to documentation generation. 2014-11-05 00:32:23 +08:00
gatk-queue-extensions-generator Split all imports of tools|engine from utils, and all tools from engine. 2014-10-24 20:59:46 +08:00
gatk-queue-extensions-public Adding Axiom_Exome_Plus.sites_only.all_populations.poly.vcf to the resource bundle because it is used in the v3.3 best practices 2015-01-05 14:52:31 -05:00
gatk-root Added GATKVCFConstants and GATKVCFHeaderLines to consolidate the GATK-specific VCF annotations 2015-01-13 21:32:09 -05:00
gatk-tools-public Added GATKVCFConstants and GATKVCFHeaderLines to consolidate the GATK-specific VCF annotations 2015-01-13 21:32:09 -05:00
gatk-utils Edits to work with the latest htsjdk release: 2015-01-13 21:32:10 -05:00
gsalib Updated gsalib version to 2.1 for resubmitting with updated license to CRAN 2014-12-09 17:07:48 -05:00
java/config Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
package-tests Split all imports of tools|engine from utils, and all tools from engine. 2014-10-24 20:59:46 +08:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
repo Added GATKVCFConstants and GATKVCFHeaderLines to consolidate the GATK-specific VCF annotations 2015-01-13 21:32:09 -05:00
src/main Added faster built executable, non-packaged jars. 2014-11-05 00:30:46 +08:00
pom.xml Update pom versions to mark the start of GATK 3.4 development 2014-10-23 22:31:44 -04:00