Commits

Branch selector

master

User selector

All users

All time

Commit history

Commits on Apr 10, 2020

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

  marcus1487

  committed
  1e2e996View commit details

  Copy full SHA for 1e2e996

  Browse repository at this point

Commits on Feb 21, 2020

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

  marcus1487

  committed
  c4561e0View commit details

  Copy full SHA for c4561e0

  Browse repository at this point

Commits on Feb 20, 2020

• Bump version.

  marcus1487

  committed
  9a3b7c0View commit details

  Copy full SHA for 9a3b7c0

  Browse repository at this point

Commits on Sep 30, 2019

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

  marcus1487

  committed
  87e3be1View commit details

  Copy full SHA for 87e3be1

  Browse repository at this point

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

  marcus1487

  committed
  32fdd61View commit details

  Copy full SHA for 32fdd61

  Browse repository at this point

Commits on Sep 18, 2019

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

  marcus1487

  committed
  7efbc2dView commit details

  Copy full SHA for 7efbc2d

  Browse repository at this point

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.

  marcus1487

  committed
  b509b4dView commit details

  Copy full SHA for b509b4d

  Browse repository at this point

Commits on Jul 8, 2019

• Fix bug in read_id statisitcs storage. Fixes #159

  marcus1487

  committed
  388e79dView commit details

  Copy full SHA for 388e79d

  Browse repository at this point

Commits on Jul 5, 2019

• Workaround for mappy memory leak.

  marcus1487

  committed
  0805531View commit details

  Copy full SHA for 0805531

  Browse repository at this point

Commits on Jun 18, 2019

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

  marcus1487

  committed
  2548fe5View commit details

  Copy full SHA for 2548fe5

  Browse repository at this point

Commits on Jun 17, 2019

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

  marcus1487

  committed
  67cd88eView commit details

  Copy full SHA for 67cd88e

  Browse repository at this point

Commits on Jun 14, 2019

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

  marcus1487

  committed
  ec0966cView commit details

  Copy full SHA for ec0966c

  Browse repository at this point

Commits on Jun 10, 2019

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

  marcus1487

  committed
  f3c2eccView commit details

  Copy full SHA for f3c2ecc

  Browse repository at this point

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

  marcus1487

  committed
  22a3105View commit details

  Copy full SHA for 22a3105

  Browse repository at this point

Commits on May 28, 2019

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

  marcus1487

  committed
  4528c6dView commit details

  Copy full SHA for 4528c6d

  Browse repository at this point

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

  marcus1487

  committed
  c567725View commit details

  Copy full SHA for c567725

  Browse repository at this point

Commits on May 9, 2019

• Merge pull request #176 from Shians/master

  Show description for 380b511
  marcus1487

  authored
  380b511View commit details

  Copy full SHA for 380b511

  Browse repository at this point

• Added output argument

  Shians

  committed
  cd25729View commit details

  Copy full SHA for cd25729

  Browse repository at this point

• Added documentation

  Shians

  committed
  b923a15View commit details

  Copy full SHA for b923a15

  Browse repository at this point

• Changed dump_per_read_statistic.py to be executable

  Shians

  committed
  4b45e9aView commit details

  Copy full SHA for 4b45e9a

  Browse repository at this point

Commits on May 8, 2019

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

  marcus1487

  committed
  25c7279View commit details

  Copy full SHA for 25c7279

  Browse repository at this point

Commits on May 7, 2019

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

  marcus1487

  committed
  f4804aeView commit details

  Copy full SHA for f4804ae

  Browse repository at this point

Commits on May 1, 2019

• Merge pull request #150 from yaeba/master

  Show description for e2e847f
  marcus1487

  authored
  e2e847fView commit details

  Copy full SHA for e2e847f

  Browse repository at this point

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

  marcus1487

  committed
  f8dd515View commit details

  Copy full SHA for f8dd515

  Browse repository at this point

Commits on Apr 22, 2019

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

  marcus1487

  committed
  6ced4e3View commit details

  Copy full SHA for 6ced4e3

  Browse repository at this point

Commits on Feb 22, 2019

• fix c_calc_llh_ratio_const_var

  Show description for 74f87a9
  yaeba

  authored
  74f87a9View commit details

  Copy full SHA for 74f87a9

  Browse repository at this point

• fix --standard-log-likelihood-ratio

  Show description for 27c10ef
  yaeba

  authored
  27c10efView commit details

  Copy full SHA for 27c10ef

  Browse repository at this point

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.

  marcus1487

  committed
  273fad8View commit details

  Copy full SHA for 273fad8

  Browse repository at this point

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.

  marcus1487

  committed
  8b15d08View commit details

  Copy full SHA for 8b15d08

  Browse repository at this point

Commits on Jan 15, 2019

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

  marcus1487

  committed
  b177e55View commit details

  Copy full SHA for b177e55

  Browse repository at this point

Commits on Dec 18, 2018

• Update to README.

  marcus1487

  committed
  df1b71fView commit details

  Copy full SHA for df1b71f

  Browse repository at this point

Commits on Dec 12, 2018

• Fixed bug when outputting sd or dwell text files.

  marcus1487

  committed
  5ca8b50View commit details

  Copy full SHA for 5ca8b50

  Browse repository at this point

Commits on Nov 20, 2018

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

  marcus1487

  committed
  cbb68c9View commit details

  Copy full SHA for cbb68c9

  Browse repository at this point

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…

  Show description for f08b1af
  marcus1487

  committed
  f08b1afView commit details

  Copy full SHA for f08b1af

  Browse repository at this point

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.

  marcus1487

  committed
  5804f61View commit details

  Copy full SHA for 5804f61

  Browse repository at this point