bthomas 9d6a341d15 Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose. ... Note: the -L argument takes both interval strings and filenames. If you specify an interval string that is also a file, an error will be thrown to move the file: ie. if you have a file "chr1" in the parent directory, GATK will ask you to move/delete it. But, this only happens with interval string arguments, NOT with intervals that are contained in files, which is a majority of the use case. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3602 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-21 21:49:41 +00:00
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IntervalFileMergingIterator.java	A simple utility class that implements a merging Iterator<GenomeLoc> built over an interval or bed file (this is NOT a rod, but rather a direct line-by-line file reader that converts strings to genome locs on the fly and merges overlapping intervals)	2010-06-14 15:54:37 +00:00
IntervalMergingRule.java	Refactoring intervals, separating the process of parsing interval lists,	2010-04-13 15:50:38 +00:00
IntervalUtils.java	Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose.	2010-06-21 21:49:41 +00:00