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broadinstitute / hellbender
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Repo Added 06 Jan 2015 07:33PM UTC
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LAST BUILD ON BRANCH dr_dynamic_window_in_referencecontext
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pending completion
213

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travis-pro

droazen
Allow reference window in ReferenceContext objects to be set dynamically by tools

Some tools need to dynamically resize the reference context window based upon other
input. This commit exposes a setWindow() method to allow tools to do this.

-To change the reference context size, tools should invoke setWindow() on the
 ReferenceContext provided by the engine before invoking getBases()/getBasesIterator().

-Hopefully eliminates the need for tools to create their own reference readers

-ReferenceContext still caches previous query results, but cache gets invalidated
 every time the window size changes.

Resolves #131

13 of 13 new or added lines in 1 file covered. (100.0%)

7531 of 11822 relevant lines covered (63.7%)

0.64 hits per line

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213 dr_dynamic_window_in_referencecontext Allow reference window in ReferenceContext objects to be set dynamically by tools Some tools need to dynamically resize the reference context window based upon other input. This commit exposes a setWindow() method to allow tools to do this. -To ... push 22 Jan 2015 05:58PM UTC droazen travis-pro pending completion  
204 dr_dynamic_window_in_referencecontext Allow reference window in ReferenceContext objects to be set dynamically by tools Some tools need to dynamically resize the reference context window based upon other input. This commit exposes a setWindow() method to allow tools to do this. -To ... push 21 Jan 2015 08:59PM UTC droazen travis-pro pending completion  
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