aaron af440943a4 Fixing a bug that Steven uncovered; we had an abigous contract for peek() in PushbackIterator, and SeekableRODIterator wasn't checking to see if it's PushbackIterator hasNext() was true before calling peek(). ... Changed peek() to element() to be consistant with the Java standards of the Queue and Stack classes (element() throws an exception if a record isn't available). Also updated some of the ROD iterator next() methods to throw NoSuchElementException if next() is called when a record isn't available. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2372 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-15 23:04:40 +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/org/broadinstitute/sting	Fixing a bug that Steven uncovered; we had an abigous contract for peek() in PushbackIterator, and SeekableRODIterator wasn't checking to see if it's PushbackIterator hasNext() was true before calling peek().	2009-12-15 23:04:40 +00:00
test/org/broadinstitute/sting	Pull the genotype (and genotype quality) calculation out of the VCF code and into the Genotyper.	2009-12-15 04:29:28 +00:00