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Altius / hotspot2

Implementation of hotspot2 by Eric Rynes
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tallyCountsInSmallWindows.cpp assumes chromSizes file has 2 columns (not BED input) #10

Closed erynes closed 8 years ago

erynes commented 8 years ago

I've been working with files of chromosome sizes of the form

chr1 249250621 chr2 243199373 etc.

Currently, tallyCountsInSmallWindows.cpp assumes input in this format, with the ordering (presumably either {chr1, chr2, etc.} or sort-bed order) immaterial. Function loadChromSizes() should count columns and allow for either this format or BED (3-column) format.

erynes commented 8 years ago

Closed via commit 2aa3c35c2a41f9d55bb6ad56c1924707fa9f2d80.