AbstractBAMFileIndex.query array list optimization #4
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Hi Beat, I pulled down your changes, rebased them, submitted another pull request, and merge it. -Alec |
jmthibault79
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Mar 26, 2019
# This is the 1st commit message: move Container.setByteOffset() call inside ContainerIO.readContainer() - also ContainerHeaderIO.readContainerHeader() restrict access to setByteOffset() and encapsulate Container.slices # This is the commit message #2: oops # This is the commit message #3: a little unrelated cleanup # This is the commit message #4: oops # This is the commit message #5: better CRAIEntryTest # This is the commit message #6: test improvements and a fix # This is the commit message #7: comment # This is the commit message #8: javadoc # This is the commit message #9: review comments # This is the commit message #10: comments and clarification for CRAMBAIIndexer
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I was having some performance problems when using getSpanOverlapping. I identified one of the issues to be the creation of many unneeded empty Arraylists in the query function. This patch only creates an arraylist when it is actually needed, otherwise the much faster Collections.emptyList() is used.
In my usecase i saw a 40% speedup, this may be different on different datasets, but there should be no reason for any performance decrease in any situation.