OpenSwathMzMLFileCacher

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 -- This tool caches the spectra and chromatogram data of an mzML to disk.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

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
                     
Common UTIL 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

+OpenSwathMzMLFileCacherThis tool caches the spectra and chromatogram data of an mzML to disk.

version2.3.0 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

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 Overwrite tool specific checks.true,false

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