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Changelog

2.7.1 (2024-08-23)

  • Added Conda environment.yml.
  • Fixed bugs:
    • Corrected N50 and L50 computation (issue #28).
    • Recognized the standard barcode arrangement (BC|RB|NB|BP) in the samplesheet (issue #27).
    • Fixed barcoding for the Fastq_extractor (issue #30).
    • Fixed time format for BAM and FASTQ extractors.

2.7 (2024-06-21)

  • Moved to Ubuntu 24.04.
  • Added support for ONT samplesheet.
  • ToulligQC now recognizes the barcode column name as 'barcode'.
  • ToulligQC now supports irregular barcode naming; issue #22.
  • Fixed bugs:
    • Pandas inplace issue for FASTQ and onedsquare summary files.
    • PlotlyJS inclusion for independent image exports.
    • Corrected read/base count histogram.
    • Handled empty lines in FASTQ file.
    • Resolved compression issue in pod5 file.
    • BAM extractor can now deal with any BAM, even if it has not been generated by Dorado.
    • Handled barcode name when it's associated with kit_barcode.

2.6 (2024-01-26)

  • Support for the POD5 format.
  • Handling of barcoding in BAM and FASTQ files.
  • Support for Fast5 .tar files without compression.
  • Fixed an issue with BAM tags extraction.
  • Fixed the issue with the 'passes_filtering'-only sequencing summary.
  • Fixed the bug related to numpy.bool with numpy version 1.24 or later.
  • Improved compatibility with pandas 2.0.

2.5 (2023-11-03)

  • Fixed error when no failed reads were found (Issue #20).
  • Fixed error when unclassified barcodes were missing.
  • FASTQ and BAM files can now be used instead of the sequencing summary file.
  • Added the ability to specify a barcode range (e.g., --barcodes barcode01:barcode48).

2.4 (2023-04-26)

  • In over time graphs (read length, PHRED score and translocation speed), now fill the gaps for the 75% and 25% to avoid filling glitch.
  • Fix 2D density plot title style.
  • Fix error when a summary file with barcode information was provided in addition of barcoding files (Issue #17), now the barcode files will be skipped with a warning message in case summary file with barcode information is provided.
  • Add the selected speed and sample frequency of the run in the "Run statistics" table of the ToulligQC report

2.3 (2023-03-22)

  • Numpy 1.24 is now supported (thanks to Sean Black).
  • Scatter plot of read length vs PHRED score has been replaced by a 2D density plot.
  • Add bases per barcode distribution graphs.

2.2.3 (2022-09-29)

  • Fix error when no Fast5 file is found in a directory provided as argument. Now throw an understandable error message.

2.2.2 (2022-08-31)

  • Fix when multiple sequencing summary barcode files were available, the type of the 'barcode_arrangement' column in the dataframe was not correct.

2.2.1 (2022-01-05)

  • Generated images were not included in the main HTML report file.

2.2 (2022-01-03)

  • Add some flexibility to barcode specification (Thanks to Hunter Cameron).
  • The sequencing_summary.txt and sequencing_telemetry.js files can now be read compressed in gzip or bzip2.
  • Add some log information on stdout for duration of the sequencing summary extractors.
  • Change the format of the duration in log.
  • Now logs memory used by dataframes.
  • Fix Docker image build issue when updating setuptools.
  • QScores and durations are now stored in 32 bits floats instead of 64 bits to reduce memory consumption (≈25% for 1D data).
  • Barcode arrangements are now stored as categories instead of strings.

2.1.1 (2021-08-18)

  • Fix issue when barcode list argument contains non existing barcode(s) in input data or when all existing barcodes are used.

2.1 (2021-06-28)

  • The channel occupancy of the flowcell graph code has been rewritten to use Plotly. Add all/pass/fail/fail ratio views. The flowcell graph can now also handle Flongle and PromethION flowcels in addition of standard MinION flowcell
  • Add "Sequencing kit" and "Barcode kits" entries in the run statistics table in html report
  • In the distribution of read lengths graph, add buttons to show base count distribution in linear/log modes.
  • Fix scatterplot graph where the default max x-axis value was always the max value for fail reads
  • Fix help links in demo report
  • Fix the name of the "Device and software" and "Run statistics" sections

2.0.1 (2021-04-14)

  • In setup.py, set the developement status for ToulligQC as Production/Stable instead of Beta
  • Add MANIFEST.in file to add resources files in PyPi package
  • Fix error with latest versions of NumPy by add a missing int casting

2.0 (2021-04-09)

  • Fix duration computation
  • For PHRED score distribution boxplots, remove unnecessary interpolation before creating boxplot
  • Remove duplicated code for 1D and 1D2 in PHRED score distribution graphs
  • Remove duplicated code for 1D and 1D2 in Correlation between read length and PHRED score graphs
  • In read length distribution graphs, add buttons to switch between linear and log scale for xaxis
  • Add minimal qscore threshold in the "Device and software information" report table
  • In 1D/1D2 sequencing summary extractors, now replace NA values for barcode assignment by "unclassified". Print a warning message on console
  • Update unit tests
  • For read count histogram tables, replace "frequency" by "percent"
  • Rename y-axis for "Distribution of read lengths" graphs to "Read count"
  • Add new command line options to finely define output file paths
  • Update the sigma value for gaussian filters when smoothing plots
  • In correlation scatterplots, now ponderate the number of pass/fail spots by the pass/fail ratio when using interpolation

2.0b3 (2021-03-22)

  • New CSS for HTML report
  • Add new plots (Read length and PHRED over time, translocation speed...)
  • Enhancement of existing graphs
  • Big refactoring code for sequencing summary file parsing
  • Big refactoring code for creating plots
  • Reduce memory usage and execution time with barcodes
  • Fix Plotly dependency version requirement
  • Add L50 computation
  • Sequence lengths of reads was stored into np.int16 that cannot handle >=32kb reads. Now use np.uint32
  • Add ToulligQC logo in HTML report
  • A telemetry file or Fast5 file is no more required
  • Add new fields in the two first tables of the report: Run ID, operating system and basecalling date
  • Barcode distribution pie charts can now be visualised as histograms
  • In table, float values have now comma separator for thousands
  • Update the yield number format in run statistocs table
  • Update colors in the graphs
  • Add an information link in all the graph titles

2.0b2 (2020-11-20)

  • Fix import bug
  • Fix graph names partially hidden in HTML summary element
  • Rewrite help and rename arguments for clarity
  • Create required and optional argument groups
  • Create default values for --report-name and --output command line arguments
  • Update report.html example in Docs with the new version of ToulliQC
  • Create new presentation image for README

2.0b1 (2020-11-17)

  • Refactoring of the sequencing_summary_extractor
  • Refactoring of the 1dsqr_sequencing_summary_extractor
  • Many performance improvements (reducing memory usage)
  • Graphs are now made with Plotly
  • Removal of unused options (Albacore log, FASTQ files, configuration file and samplesheet file)
  • N50 information added to report.html
  • Removal of Albacore support
  • Now handle PromethION data
  • Update of required dependencies versions
  • Add unit tests
  • Add new plots (throughput sequencing time)
  • Update graph colors

1.3 (2019-11-07)

  • Add a --barcodes option that allow to avoid samplesheet file creation
  • The size of the graphs are now set to 1000x600px
  • Many small fixes in graph generation (remove titles, fix grids and layouts...)
  • In the HTML report, replace the tooltip icon by an unicode character

1.2 (2019-07-25)

  • MultiFast5 file can now be used to retrieve run information
  • Reporting other barcodes in the "other" category
  • Gathering information from Telemetry files in the HTML report

1.1 (2019-03-21)

  • Add Guppy support for 1D and 1D2
  • Telemetry files generated by Albacore or Guppy can now be used to retrieve run information instead of reading a FAST5 file and the pipeline.log file.
  • Refactoring of the code of the extractors

1.0 (2018-10-23)

  • Report.data log file reviewed

0.10 (2018-07-18)

  • Add pipeline.log parsing option

0.9 (2018-03-21)

  • Fix out of memory error when parsing big FASTQ files. The parsing of FASTQ files is now faster

0.8 (2018-03-14)

  • Fix unexisting import in toulligqc.py
  • Fix the not working "--quiet" option

0.7 (2018-03-14)

  • Fix Dockerfile that used the Ubuntu 17.04 (Ubuntu 17.04 packages repository is no more available)

0.6 (2018-03-12)

  • Update html.report for 1D and 1Dsquare data
  • Fix issue when processing fast5 files directory
  • Add pass/fail filter
  • Add extractor and graphs for 1dsquare analysis

0.5 (2017-11-28)

  • Fix exception when toulligqc was launched with no arguments
  • Remove pypandoc dependency in setup.py
  • Fix issue when checking if directory paths ends with a '/'
  • Fix issue when checking missing arguments

0.4 (2017-11-27)

  • Fix issue with the --version option of ToulligQC

0.3 (2017-11-27)

  • Fix issue with setup.py and pip install

0.2 (2017-11-27)

  • ToulligQC can now handle Albacore 2.0 output
  • The run date is now extracted from a FAST5 file
  • Update setup.cfg for PyPi package submission
  • Update ToulligQC documentation

0.1 (2017-08-30)

  • Initial version