Back online, up to date, with minor updates

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Bogdan

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Jul 30, 2011, 4:33:49 PM7/30/11
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Earlier this year Cotrasif was disabled when a problem was discovered with newly-submitted tasks. The problem was a consequence of upgrading server OS and all the system software/libraries, which then required recompiling tool binaries.

As of this writing, Cotrasif is back online and ready to serve, with an up-to-date DB of promoters.

  • Downloadable binaries now support tab as column separator in PFM files. Previously, only space-separated values were allowed (tab-separated files were truncated after the first column).
  • The status of the 32bit downloadable binary is now "not maintained" ("Downloads" page will be updated soon to reflect this change). Though that version does undergo automatic testing, the focus is on the 64-bit version.
  • Despite the "--strand" option described in the output of "--help" of the binaries, that feature is not yet complete and will fail if used.
  • The long-lasting problem with zeros in fractional PFMs got a new, better fix, which should marginally improve search specificity. Zero values in the user-submitted fractional PFMs are now replaced with the whole-matrix minimal non-zero value, divided by 4. Previously, a constant position penalty was used.
More exciting updates to follow soon.
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