Geraldine Van der Auwera faef85841b Added GATKDocs fct to indicate default Read Filters for each tool ... -- Added getClazzAnnotations() as hub to retrieve various annotations values and class properties through reflection -- Added getReadFilters() method to retrieve Read Filter annotations -- getReadFilters() uses recursion to walk up the inheritance to also capture superclass annotations -- getClazzAnnotations() stores collected info in doc handler root, which is unit.forTemplate in Doclet -- Modified FreeMarker template to use the Readfilters info (displayed after arg table, before additional capabilities) -- Tadaaa :-) #GSATDG-63 resolve		2013-02-19 16:12:29 -05:00
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R	Fix a nasty bug in reading GATK reports with a single line	2012-09-10 20:14:13 -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	…
java	Added GATKDocs fct to indicate default Read Filters for each tool	2013-02-19 16:12:29 -05:00
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	Message "script failed" moved to the correct place in the code	2013-02-04 15:37:23 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00