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Gene Selkov, Jr. > Finnigan > uf-index


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uf-index - examine the ScanIndexEntry structures in a Finnigan raw file


uf-index [options] file


  -a[ll]                        process all existing index entries
  -n[unmber] <n>                get one index entry number <n>
  -range <from> .. <to>         extract all entries with numbers between <from> and <to>
  -d[ump]                       dump all data in each index entry 
  -s[ize]                       print object size 
  -h[tml]                       dump as html 
  -w[iki]                       dump in wiki table format 
  -r[elative]                   show relative addersess in dump 
  -f[ormat] <type>              format the unknown long as 'bin', 'hex', or 'ms' (for MS level)
  <file>                        input file 



Print a brief help message and exits.


Prints a table listing all fields in the ScanIndexEntry records, with their seek addresses, sizes, names and values. Individual entries can be selected with the -n[umber] option or with the -range option.


Gives the number of a single ScanIndexEntry to process


Selects a range of the ScanIndexEntry records to process


Format the dump output as an html table. When multiple entries are specified, each will be rendered in its own table


Format the dump output as a wiki table.


Show structure size in bytes (works with the -d[ump] option).


Show relative addresses of all itmes in the dump. The default is to show the absolute seek address. (works with the -d[ump] option)


Process all entries, including those that may lie outside the declared range. It appears as though it can be possible to find more index entries in the file than would fit between the first and the last scan numbers specified in RunHeader/SampleInfo. In that case, in the absence of the -all option, the entries will be enumerated according to ScanIndex, which will be treated as a linked list -- starting with the entry whose index matches the first scan number.


uf-index can be used to dump the scan index entries from a Finnigan raw file.




Print all index entries in the file in a tabular form:
  uf-index sample.raw 
Print the first five records:
  uf-index -range 1 .. 5 sample.raw
Show individual bits in the scan type word:
  uf-index -range 1 .. 5 -format bin sample.raw
Dump the fifth index entry with relative addresses and shows its size:
  uf-index -rdsn 5 ~/shared/test/sample4.raw 
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