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jibsch / Socrates

Socrates: Identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads
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Debugged #2

Closed alhsu closed 11 years ago

alhsu commented 11 years ago

Arthur's new version.

Fixed duplicated breakpoints. Fixed cleaning up of temporary files. Fixed exception handling. Fixed single-end data bugs.

Updated the driver script:

  1. got rid of intermediate shell driver script and is fully Pythonic.
  2. JVM memory is as script option and performs a rough required memory check.
  3. changes to subprocess calls that should take care of potential blocking of script.