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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.

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

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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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Commits on May 28, 2019

• 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 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 Feb 22, 2019

• fix c_calc_llh_ratio_const_var

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• fix --standard-log-likelihood-ratio

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Commits on Jan 30, 2019

• Added error logic to catch processes where the io/mapping thread to resquiggle process connection has died. Attempt to fix new issue in #139.

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Commits on Jan 28, 2019

• Added signal and sequence length filters to address some long direct RNA run times and memory overflow. Fixes #139. Potentially a fix for #111.

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Commits on Jan 15, 2019

• Fixed missing preprocess several places in the docs. Fixes #138.

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Commits on Dec 12, 2018

• Fixed bug when outputting sd or dwell text files.

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Commits on Nov 20, 2018

• Fixes #130. Bug in mean signal output when control sample is not provided.

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Commits on Nov 5, 2018

• Fixes #125 where zero-SD sites cause a division by zero in model sample compare method and fixes #127 where sequence extracted for motif_with_stats throws an error when attempting to extract sequen…

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Commits on Oct 24, 2018

• Fixed issue when the base fast5 directory has the same name as a sub-directory in the fast5s file storage structure. Fixes #124 and fixes #109.

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Commits on Oct 12, 2018

• Version 1.5 release. This release includes two major feature additions. The first is motif-specific model (packaged with CpG, dam and dcm models) which provide more accurate detection of modificati…

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Commits on Sep 10, 2018

• Removed debugging flag left on in the FAST5 handling code for corrupted file detection.

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Commits on Aug 1, 2018

• Version 1.4 release. This release includes major improvements to RNA signal processing (via resquiggle command), a major re-write of the Tombo python API, and use of the canonical model as a prior …

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Commits on Jun 26, 2018

• Fixed typo from #73 fix. Fixes #75.

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Commits on Jun 21, 2018

• Addresses hanging process in pre-processing command from unlimited filename queue size, similar to #70. Fixes #73.

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Commits on Jun 18, 2018

• Fixed bug due to unlimited queue size which hangs on some systems for large runs. Fixes #70.

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Commits on May 29, 2018

• Minor omissions from quick start guide in README and docs. Also some better error handling around the new testing command scheme.

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Commits on May 23, 2018

• Version 1.3 release. This release includes updates to signal normalization procedure (including sequence-dependent iterative re-scaling) and an outlier-robust alternative model comparison method. T…

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Commits on Apr 17, 2018

• Fixes #57. Checking genome index in write_most_significant_fasta assumed pyfaidx index. Fixed to add __contain__ method to Fasta class for handling either pyfaidx or raw text Fasta access.

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Commits on Mar 20, 2018

• Minor fixes for some python2 bugs. Addressed #42. Fixes #41.

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