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gotcloud.1.11
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@mktrost mktrost released this 11 Sep 20:38
· 453 commits to master since this release
gotcloud.1.11
37a42ae

Aligner

  • Remove an extra space from the Makefile for the dedup command.
  • Brought in latest bwa source, but it is not yet being used.

Variant Calling

  • Rename OUT_PREFIX to MAKE_BASE_NAME to specify the base filename for snpcall, ldrefine (beagle & thunder), & vc Makefiles. The typeOfRun.Makefile is appended to MAKE_BASE_NAME.
    • These Makefiles all used to have the same name and would overwrite each other
    • --makebasename/--make_basename/--make_base_name can be specified on the command-line
    • Default value for MAKE_BASE_NAME is umake
      • snpcall is now: $(MAKE_BASE_NAME).snpcall.Makefile (default umake.snpcall.Makefile)
      • ldrefine beagle step is now: $(MAKE_BASE_NAME).beagle.Makefile (default umake.beagle.Makefile)
      • ldrefine thunder step is now: $(MAKE_BASE_NAME).thunder.Makefile (default umake.thunder.Makefile)
      • vc is now: $(MAKE_BASE_NAME).vc.Makefile (default umake.vc.Makefile)
  • Added gotcloud beagle and gotcloud thunder commands so that beagle/thunder can be called independently rather than just through ldrefine.
  • Add command-line options to gotcloud vc for running just certain steps rather than having to set RUN...=true in the configuration
    • More than one --commandToRun can be specified at once
    • New commands-line options:
      • --index (or RUN_INDEX = true in the configuration file)
      • --pileup (or RUN_PILEUP = true in the configuration file)
      • --glfMultiples (or RUN_GLFMULTIPLES = true in the configuration file)
      • --vcfPileup (or RUN_VCFPILEUP = true in the configuration file)
      • --filter (or RUN_FILTER = true in the configuration file)
      • --svm (or RUN_SVM = true in the configuration file)
      • --split (or RUN_SPLIT = true in the configuration file)
  • Cleaned up the snpcall Makefile entries for pileup. It used to print targets/commands that were never executed. These unused targets have now been removed

Aligner & Variant Calling

  • Remove trailing spaces from configuration values
  • Add MAKE_OPTS configuration value that allows users to add Makefile options to the make calls that run the pipelines.
  • Update gccalcstorage for better estimates and to have option to print estimates from a starting size rather than from actually input files
Assets 2