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Commits on Nov 19, 2021

• Printing dev version message

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Commits on Jul 30, 2020

• Forgot to commit resquiggle.py

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• Added cigar attribute in alignment group

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Commits on Jun 16, 2020

• Add file mode to h5py in preprocessing. Addresses #263.

  marcus1487

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Commits on May 28, 2020

• Merge branch 'master' of https://github.com/nanoporetech/tombo

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• Fix logic for filtering statistic browser outputs. Partially addressing issue in #256.

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Commits on May 27, 2020

• Add flag to use cowplot in plot motif_with_stats since aligned grid seems unstable.

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• Added I/O and read mapping profiling.

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• Allow per-read aggregation for sample compare methods. Fixes #246.

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Commits on Apr 10, 2020

• Make observations per-base value required for stuck filtering command.

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Commits on Feb 21, 2020

• Catch case when valid coverage only intersects edge of region when computing statistics.

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Commits on Feb 20, 2020

• Bump version.

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Commits on Sep 30, 2019

• Fix output of "Invalid warning code encountered" errors in preprocess script.

  marcus1487

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• Fix bug in region read means extraction. Fixes #209.

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Commits on Sep 18, 2019

• Pin rpy2 version to <=2.9.5 as rpy2 v3 has caused several issues. Fixes #208. Fixes #212.

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Commits on Jul 10, 2019

• Added note on lack of multi-fast5 support to function which trys to retrieve raw data slot (should be first access point for most all workflows). Addressed #194.

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Commits on Jul 8, 2019

• Fix bug in read_id statisitcs storage. Fixes #159

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Commits on Jul 5, 2019

• Workaround for mappy memory leak.

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Commits on Jun 18, 2019

• Move numpy divide by zero ignore to the correct scope. Addressing #188.

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Commits on Jun 17, 2019

• Catch error around taking log of zeros. Fixes #188.

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Commits on Jun 14, 2019

• Fix file read mode for model estimation function. Potentially related to #179 .

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Commits on Jun 10, 2019

• Add warning and error messages when ground truth and stats files don't correspond. Addresses #177.

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• Add note to docs concerning level sample compare statistic output.

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Commits on May 28, 2019

• Merge branch 'master' of https://github.com/nanoporetech/tombo

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• Report incorrectly formatted BED location files. Previous behavior silently ignored misformatted lines. Also added note in docs for expected file format.

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Commits on May 9, 2019

• Merge pull request #176 from Shians/master

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• Added output argument

  Shians

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• Added documentation

  Shians

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• Changed dump_per_read_statistic.py to be executable

  Shians

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Commits on May 8, 2019

• Added script to dump per-read statistics to text file. Fixes #174.

  marcus1487

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Commits on May 7, 2019

• Added better argument enforcement around plot roc command. Fixes #175

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Commits on May 1, 2019

• Merge pull request #150 from yaeba/master

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• Fix issue in text output command when attempting to extract sequence beyond the end of a chromosome. Addresses second issue in #127.

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Commits on Apr 22, 2019

• Added note to README concerning support for multi-FAST5.

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Commits on Feb 22, 2019

• fix c_calc_llh_ratio_const_var

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  yaeba

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