Thread: maq merge limit
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Old 09-04-2009, 08:18 AM   #2
Nils Homer
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Originally Posted by Layla View Post

Is there a limit to the number of map files that can be merged using
./maq mapmerge? If so, is there a way to overcome this for short paired end reads?


I would assume the limit is the maximum number of arguments generally a command line tool can accept (argv & argc stuff), which is in the thousands. Anyhow, if you have millions of .map files, I would ask why? If you truly have millions of .map files you could just do the merge step of merge sort whereby you group .map files into pairs of .map files and merge each pair, rinse and repeat. Again, how many .map files do you have?

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