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Commits on Jun 19, 2019

• Merge pull request #126 from DavyCats/dc_gffparser_fix_crash_on_gene_line

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Commits on Feb 6, 2013

• Nicer fix.

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  115b1cd

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• Fixed the sam->bam conversion step.

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Commits on Feb 2, 2013

• Removed not.

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  f89a3ee

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• Fix to estimate the proper inner distance with Bowtie2.

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• Changed free memory lookup to using psutil instead of free for portability.

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Commits on Jan 18, 2013

• Updated to use the new memoization.

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• Added a fastq groomer to play with the updated memoization.

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• Refactor of memoize output to take either ext or stem as an argument and do the right thing.

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Commits on Jan 16, 2013

• Added unit tests for the updated decorators.

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• Memoize returns the output from the function it decorates if the function runs.

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• Changed decorator signatures to more closely match the originals.

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• Refactor @memoize_outfile to not also transform the filename.

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Commits on Jan 15, 2013

• Refactor to make it easier to follow.

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Commits on Jan 14, 2013

• Added arbitratry options passing.

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• Added reading option list from tophat resources.

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  a2d4835

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Commits on Jan 11, 2013

• Switched from throwing exceptions to exiting since there is nothing to handle.

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Commits on Jan 10, 2013

• Added Tophat 2 support.

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Commits on Jan 9, 2013

• Merge branch 'master' of https://github.com/chapmanb/bcbb

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Commits on Dec 12, 2012

• Added split_vcf plus a unit test.

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• Merge branch 'master' of https://github.com/chapmanb/bcbb

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Commits on Dec 2, 2012

• Added is_sequence and is_pair for checking if input is from paired end

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Commits on Nov 29, 2012

• Added pushing the logging handler to the engines on cluster startup.

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• Pared down the unit test data to about 5k reads on a single gene.

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• Unit test for bed12 -> picard interval conversion.

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  ca456dd

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• Added some data files for unit tests.

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• Added documentation.

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Commits on Nov 28, 2012

• Added get_in for looking up nested dictionaries with tuples.

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Commits on Nov 27, 2012

• Merge branch 'master' of https://github.com/chapmanb/bcbb

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Commits on Nov 21, 2012

• Added convenience functions replace_suffix and append_stem.

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• Merge branch 'master' of https://github.com/chapmanb/bcbb

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Commits on Nov 9, 2012

• Added file_transaction.

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• Added bed2interval.

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Commits on Nov 2, 2012

• Merge branch 'master' of github.com:roryk/bcbb

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• Added parsing of CollectRnaSeqMetrics output.

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