v2.1.2

This release fixes an edge-case premature exit that could occur in wavelet resolution.

v2.1.1

This release improves the handling of very small and very large numbers at loci where the input data might become extreme.

v2.1

This release adds functionality for optionally identifying variable-width "peaks" within hotspots, the latter of which may occasionally be statistically significant across a somewhat wide stretch of contiguous bp (e.g. ~2kb). These variable-width peaks can be supplied as input to our software for building an "index" or "master list" of DHSs from a collection of samples (github Altius/Index). This release also contains a fix for an "underflow" issue in FDR reporting, as well as other minor improvements.

Please be sure to build all hotspot2 binaries from this release before running hotspot2. Note that two new programs have been added to report variable-width peaks: findVarWidthPeaks and resolveOverlapsInSummit-CenteredPeaks.

v2.0

New features and improvements:

• FDR now estimated globally (all P-vals) rather than locally (batches of 1M)
• Fixes score reporting in narrowPeak format of hsmerge.sh output
• Improved (and now non-overlapping) peak calling from hotspots
• Improved definition of "center sites" (viable centers of small windows)
• "Bad spots" are now filtered out of cut counts output.

Note that hotspot2.cpp is now two executables: hotspot2_part1 and hotspot2_part2.

Hotspot2 v1.1

• Bug fixes in the creation of density and peak files
• Optional seed may be used with hotspot2.sh

Version 1.0

Initial public release of hotspot2