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DBsplit - Online in the Cloud

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This is the command DBsplit that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



DBsplit - divide a Dazzler database into a series of blocks


DBsplit [-a] [-xint] [-sint(200)] path:db|dam


Divide the database path.db or path.dam conceptually into a series of blocks referable to
on the command line as path.1, path.2, ... If the -x option is set then all reads less
than the given length are ignored, and if the -a option is not set then secondary reads
from a given well are also ignored. The remaining reads, constituting what we call the
trimmed DB, are split amongst the blocks so that each block is of size -s * 1Mbp except
for the last which necessarily contains a smaller residual. The default value for -s is
200Mbp because blocks of this size can be compared by our "overlapper" daligner(1) in
roughly 16Gb of memory. The blocks are very space efficient in that their sub-index of
the master .idx is computed on the fly when loaded, and the .bps and .qvs files (if a .db)
of base pairs and quality values, respectively, is shared with the master DB. Any
relevant portions of tracks associated with the DB are also computed on the fly when
loading a database block.

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