hanna 8e36a07bea Convert GenomeLocParser into an instance variable. This change is required ... for anything that needs to be simultaneously aware of multiple references, eg Queue's interval sharding code, liftover support, distributed GATK etc. GenomeLocParser instances must now be used to create/parse GenomeLocs. GenomeLocParser instances are available in walkers by calling either -getToolkit().getGenomeLocParser() or -refContext.getGenomeLocParser() This is an intermediate change; GenomeLocParser will eventually be merged with the reference, but we're not clear exactly how to do that yet. This will become clearer when contig aliasing is implemented. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-10 17:59:50 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
test	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00