David Roazen f9c986be74 Remove com.sun.javadoc.* dependencies from the GATK proper, and isolate them for doclet use only ... Problem: Classes in com.sun.javadoc.* are non-standard. Since we can't depend on their availability for all users, the GATK proper should not have any runtime dependencies on this package. Solution: -Isolate com.sun.javadoc.* dependencies in a DocletUtils class for use only by doclets. The only users who need to run our doclets are those who compile from source, and they should be competent enough to figure out how to resolve a missing com.sun.* dependency. -HelpUtils now contains no com.sun.javadoc.* dependencies and can be safely used by walkers/other tools. -Added comments with instructions on when it is safe to use DocletUtils vs. HelpUtils [delivers #51450385] [delivers #50387199]		2013-06-13 15:52:41 -04:00
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R	Updating gsalib for R-3.0 compatibility	2013-05-18 12:43:38 -04:00
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
chainFiles	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Remove com.sun.javadoc.* dependencies from the GATK proper, and isolate them for doclet use only	2013-06-13 15:52:41 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
testdata	Somehow the index of exampleDBSNP.vcf was missing	2013-05-28 15:29:43 -04:00