FuzzyDiff

Compares two files, tolerating numeric differences.

In the diff output, "position" refers to the characters in the string, whereas "column" is meant for the text editor.

Only one of 'ratio' or 'absdiff' has to be satisfied. Use "absdiff" to deal with cases like "zero vs. epsilon".

The command line parameters of this tool are:

FuzzyDiff -- Compares two files, tolerating numeric differences.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_FuzzyDiff.html
Version: 3.6.0-pre-nightly-2026-01-10 Jan 11 2026, 01:46:15, Revision: 244eb32
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  FuzzyDiff <options>

Options (mandatory options marked with '*'):
                       
  -in1 <file>*         First input file
  -in2 <file>*         Second input file
                       
  -ratio <double>      Acceptable relative error. Only one of 'ratio' or 'absdiff' has to be satisfied.  Use 
                       "absdiff" to deal with cases like "zero vs. epsilon". (default: '1.0') (min: '1.0')
  -absdiff <double>    Acceptable absolute difference. Only one of 'ratio' or 'absdiff' has to be satisfied. 
                        (default: '0.0') (min: '0.0')
                       
  -verbose <int>       Set verbose level:
                       0 = very quiet mode (absolutely no output)
                       1 = quiet mode (no output unless differences detected)
                       2 = default (include summary at end)
                       3 = continue after errors
                        (default: '2') (min: '0' max: '3')
  -tab_width <int>     Tabulator width, used for calculation of column numbers (default: '8') (min: '1')
  -first_column <int>  Number of first column, used for calculation of column numbers (default: '1') (min: 
                       '0')
                       
  -sort                Sort the input files before comparison (useful for tabular files where row order may 
                       vary). The first line of each file is assumed to be a header and is not sorted.
                       
Common TOPP options:
  -ini <file>          Use the given TOPP INI file
  -threads <n>         Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>    Writes the default configuration file
  --help               Shows options
  --helphelp           Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+FuzzyDiffCompares two files, tolerating numeric differences.

version3.6.0-pre-nightly-2026-01-10 Version of the tool that generated this parameters file.

++1Instance '1' section for 'FuzzyDiff'

in1 first input fileinput file

in2 second input fileinput file

ratio1.0 acceptable relative error. Only one of 'ratio' or 'absdiff' has to be satisfied. Use "absdiff" to deal with cases like "zero vs. epsilon".1.0:∞

absdiff0.0 acceptable absolute difference. Only one of 'ratio' or 'absdiff' has to be satisfied. 0.0:∞

whitelist[ Lines containing one of these strings are skipped

matched_whitelist[] Lines where one file contains one string and the other file another string are skipped. Input is given as list of colon separated tuples, e.g. String1:String2 String3:String4

verbose2 set verbose level:
0 = very quiet mode (absolutely no output)
1 = quiet mode (no output unless differences detected)
2 = default (include summary at end)
3 = continue after errors
0:3

tab_width8 tabulator width, used for calculation of column numbers1:∞

first_column1 number of first column, used for calculation of column numbers0:∞

sortfalse sort the input files before comparison (useful for tabular files where row order may vary). The first line of each file is assumed to be a header and is not sorted.true, false

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false