asivache 073fdd8ec7 Let's try not to die suffocating when a bad region with humongous coverage is encountered. New option: -maxNumberOfReads (--mnr), with default of 10,000. If count of reads cached in the current window reaches the specified limit, the whole window is immediately shifted by the whole window length and all currently cached reads are dropped. NOTE: this also means that we are not going to call ANY indels from the current window, even though we could try using just the reads cached so far. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2921 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-03 17:34:30 +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	Let's try not to die suffocating when a bad region with humongous coverage is encountered. New option: -maxNumberOfReads (--mnr), with default of 10,000. If count of reads cached in the current window reaches the specified limit, the whole window is immediately shifted by the whole window length and all currently cached reads are dropped. NOTE: this also means that we are not going to call ANY indels from the current window, even though we could try using just the reads cached so far.	2010-03-03 17:34:30 +00:00
test/org/broadinstitute/sting	a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone.	2010-03-03 16:31:45 +00:00