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Commits on Aug 1, 2018

• Update java options to reduce GC time and threads (issue marbl#993) and memory

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• update call to seq store creation

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• Fix bug which was truncating some large contigs

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Commits on Jul 26, 2018

• Merge pull request marbl#1019 from rick-heig/patch-1

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Commits on Jul 12, 2018

• Merge pull request marbl#995 from luyang93/patch-1

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Commits on Jun 20, 2018

• Update faq.rst

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• Update faq.rst

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Commits on Jun 8, 2018

• Fix paging issues checking gnuplot (issue marbl#939)

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Commits on May 25, 2018

• Use full paths to dx command

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Commits on May 22, 2018

• Stop renaming the files in overlapStore, fix a bunch of incorrect paths for overlap store building and check for files not directory existence because dna nexus describe doesn't understand folders

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Commits on May 21, 2018

• Explicitly give path to script when downloading and create any necessary folders beforehand

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• Specify executive memory/threads so we can run more things in one machine and to explicitly get the right resources

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• update fetch commands to use the right path

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Commits on May 17, 2018

• Add check for -d64/-d32 options and don't use them when not available (issue marbl#909)

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Commits on May 11, 2018

• Update app to check which region it is in and appropriately request resources to avoid mixing and crashing

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Commits on May 10, 2018

• Fix corrected/trimmed read stashing again

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• Fix overlap store stash

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Commits on May 9, 2018

• update check for existence to not throw error code up to shell to abort app

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• Fix cloud check for corrected and trimmed reads

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• Fix incorrect cloud store stashes which were causing file duplications

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• Dont try to stage global scores, they no longer exist

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• Remove bogus debugging defaults

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• don't filter azure instances

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• Add dna nexus grid environment and modifications to submit jobs.

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• Support 1-job arrays

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• Fix typos and fix abort log file parsing

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Commits on May 8, 2018

• Merge pull request marbl#899 from robvdl/fix-tutorial-typo

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Commits on Apr 27, 2018

• Add complementary bases for N (which is N), issue marbl#880 and marbl#881

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Commits on Apr 18, 2018

• Fix calls to gkpStore and switch to -S instead of -G flags

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• Add initial support for alternate unitiggers, starting with WTDBG. Not yet tested beyond bacteria

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• If we find a read went out of bounds, try to align it anywhere in the tig

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Commits on Apr 17, 2018

• never set gridEngineArraySubmitID on PBS/PBSPro

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Commits on Apr 16, 2018

• Merge branch 'master' of github.com:marbl/canu

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• Parse error rate estimate from minimap output

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Commits on Apr 12, 2018

• Adding a new fast option using wtdbg for unitigging

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