changelog.txt

Version 1.2
August 30, 2023
Lucas Kearns <lucas.kearns@bcm.edu>, Thomas Miller <thomas.miller2@bcm.edu>
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ADDED:

Added --concat flag. This will concatenate mut and corresponding mutga files
together. By default N7-Gs do not contribute to clustering but are set to
inactive. This means that although N7-G positions do not drive clustering they will be 
solved for in the final model.

Added --activate_n7 flag. Allows n7 nucleotides to contribute to DanceMap
clustering. By default N7-G nucleotides will not contribute to clustering.

Added ability for concatenated DanceMapper runs to use RingMapper on solved models
and generate N1/3-N1/3, N1/3-N7G, and N7G-N7G rings.

CHANGED:

Updated eDMS normalization to reflect new pur and pyr normalization cases
for N7-G. Changed eDMS so highly protected N7-G regions (ares where bg is higher than
raw) are assigned a normalized reactivity of 3.32.

FIXED:

Debugged min coverage calculation to properly calculate 75% coverage
threshold.

Version 1.1
February 1, 2023
Anthony Mustoe <anthony.mustoe@bcm.edu>
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ADDED:

Added --ignore_untreated flag to ignore any untreated sample information in the
profile.txt file.

CHANGED:

Updated DMS normalization to eDMS by default. The --oldDMSnorm flag can be used 
to perform normalization using original method

Updated mincount cutoffs for pair/ring analysis to 10 to be compatible with
pair/ringmapper v1.2

Changed dependency to consolidated StructureAnalysisTools package

FIXED:

Fixed internal issues so untreated sample is now optional.