Serialize a spectra and/or chromatogram mzML file.

This class will serialize a spectra and/or chromatogram mzML file and store it in a binary format that contains ONLY the spectra and chromatogram data (no metadata).

This is implemented using the write_memdump and read_memdump functions. For reading there are 2 options

read the whole file into the OpenMS datastructures
read only an index (read_memdump_idx) of the spectra and chromatograms and then use random-access to retrieve a specific spectra from the disk (read_memdump_spectra)

Note: This tool is experimental!

The command line parameters of this tool are:

OpenSwathMzMLFileCacher -- Caches the spectra and chromatogram data of an mzML to disk.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathMzMLFileCacher.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar  7 2026, 01:46:19, Revision: c92c980
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:
  OpenSwathMzMLFileCacher <options>

Options (mandatory options marked with '*'):
  -in <file>*                Input mzML file (valid formats: 'mzML', 'sqMass')
  -in_type <type>            Input file type -- default: determined from file extension or content
                              (valid: 'mzML', 'sqMass')
  -out <file>*               Output file (valid formats: 'mzML', 'sqMass')
  -out_type <type>           Output file type -- default: determined from file extension or content
                             Note: that not all conversion paths work or make sense. (valid: 'mzML', 'sqMass'
                             )
  -convert_back              Convert back to mzML
  -lossy_compression <type>  Use numpress compression to achieve optimally small file size (attention: may 
                             cause small loss of precision; only for mzML data). (default: 'true') (valid: 
                             'true', 'false')
  -full_meta <type>          Write full meta information into sqMass file (may require large amounts of memor
                             y) (default: 'true') (valid: 'true', 'false')
                             
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

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

Name The identifier used in configuration files and on the command line.
Default value The value used if the parameter is not explicitly specified.
Description A short explanation describing the purpose and behavior of the parameter.
Tags Additional metadata associated with the parameter.
Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+OpenSwathMzMLFileCacherCaches the spectra and chromatogram data of an mzML to disk.

version3.6.0-pre-nightly-2026-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'OpenSwathMzMLFileCacher'

in Input mzML fileinput file*.mzML, *.sqMass

in_type input file type -- default: determined from file extension or content
mzML, sqMass

out Output fileoutput file*.mzML, *.sqMass

out_type Output file type -- default: determined from file extension or content
Note: that not all conversion paths work or make sense.mzML, sqMass

convert_backfalse Convert back to mzMLtrue, false

lossy_compressiontrue Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data).true, false

full_metatrue Write full meta information into sqMass file (may require large amounts of memory)true, false

lossy_mass_accuracy-1.0 Desired (absolute) m/z accuracy for lossy compression (e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy).

process_lowmemoryfalse Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML).
Note: this flag will prevent conversion from spectra to chromatograms.true, false

lowmem_batchsize500 The batch size of the low memory conversion0:∞

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