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CHANGELOG.md

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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

0.39.0 (2022-02-21)

Features

  • Make annotation header available for customized reports (#238) (e8fc664)

0.38.3 (2022-02-09)

Bug Fixes

  • Fix vcf-report allele frequency heatmap width (#236) (6f119d3)
  • Fix vcf-report read plot height when using --max-read-depth (#235) (4350a1a)

0.38.2 (2022-01-14)

Bug Fixes

0.38.1 (2022-01-06)

Bug Fixes

  • Report 1-based position in vcf-report log messages (#231) (bcf6260)

0.38.0 (2021-12-25)

Features

Bug Fixes

0.37.0 (2021-12-19)

Features

  • anonymize bam - adapt mandatory and aux fields (#219) (e6ffdea)

0.36.0 (2021-12-15)

Features

  • Use Feature before HGVSg for level 1 naming (#224) (4377e42)
  • Warn instead of panic for missing HGVSg values in vcf-report (#220) (5f16505)

Bug Fixes

  • Fix possible broken link to third stage of vcf-report (#221) (66299d2)

0.35.0 (2021-12-14)

Features

  • Add --annotation-field option to vcf-report (#211) (29719d5)

Bug Fixes

Miscellaneous Chores

0.34.0 (2021-12-11)

Features

  • Add --annotation-field option to vcf-report (#211) (29719d5)

Bug Fixes

0.33.1 (2021-12-07)

Features

0.33.0 (2021-12-06)

Features

Bug Fixes

  • Add error messages for missing annotations (#206) (6210dd2)

0.32.0 (2021-12-01)

Features

Bug Fixes

  • Fix read processing when building consensus reads (#199) (3fdcb3f)

0.31.0 (2021-11-16)

Features

  • rbt plot-bam: show position of reference base in tooltip (#196) (3711c09)

Bug Fixes

  • rbt plot-bam: Disconnect neighboring insertion markers (#197) (d322e6a)

0.30.2 (2021-11-09)

Bug Fixes

0.30.1 (2021-10-22)

Bug Fixes

  • Refine MAPQ color scheme and scale type (#189) (6f47c68)

0.30.0 (2021-10-22)

Features

  • Various alignment plot and CLI updates for vcf-report and plot-bam (#187) (8739ef1)

0.29.0 (2021-10-04)

Features

0.28.0 (2021-09-20)

Features

0.27.0 (2021-08-25)

Features

Bug Fixes

  • remove custom classification of duplicates and inversions from vcf-report

0.26.1 (2021-08-19)

Bug Fixes

  • Fix handling of softclips in cigars
  • Respect target CPU compat via rocksdb ^0.17 (#175) (b2428f5)

0.26.0 (2021-08-13)

Features

  • Add tooltip for vcf-report bar plots (#173) (fb91211)

0.25.0 (2021-08-09)

Features

  • add linkout for COSV entries to rbt vcf-report. (224a076)

0.24.1 (2021-07-16)

Bug Fixes

0.24.0 (2021-07-16)

Features

Bug Fixes

  • Missing lowercase reference bases in reports (#160) (a661da1)

0.23.0 (2021-07-07)

Features

  • New subcommand for plotting bam files (#156) (707ef77)

[0.22.0] - 2021-06-08

Changed

  • Revised rbt collapse-reads-to-fragments bam, CIGAR strings will now considered when merging reads (@FelixMoelder).

[0.21.1] - 2021-05-20

Changed

  • Further fixes for rbt vcf-report (@fxwiegand).

[0.21.0] - 2021-04-30

Changed

  • Small fixes for rbt vcf-report, e.g. for handling unexpected multiple canonical transcripts and eliminating the potential risk of receiving plots without any reads overlaying the variant when using --max-read-depth.

[0.20.5] - 2021-04-19

Changed

  • Bugfix for rbt vcf-report that stops displaying undefined values in the table-report.

Added

  • New parameter --pin-until for rbt csv-report. --pin-until pins the table until the given column such that scrolling to the right does not hide the given column and those before.

[0.20.4] - 2021-04-15

Changed

  • Fixed a JS bug in VCF report leading to an error with empty annotation fields.

[0.20.3] - 2021-03-31

Changed

  • Cosmetic changed and bug fixes for rbt csv-report.

[0.20.2] - 2021-03-19

Changed

  • Cleaned up histogram presentation for pathologic columns.

[0.20.1] - 2021-03-17

Changed

  • Added button to highlight numeric values in column histogram (rbt csv-report).

[0.20.0] - 2021-03-10

Added

  • New parameter --formatter for rbt csv-report.
  • --formatter allows the specification of custom formatting functions for one or multiple columns of the given csv file.

[0.19.7] - 2021-03-09

Changed

  • Performance improvement for rbt csv-report.

[0.19.6] - 2021-03-09

Changed

  • Fixed a JSON syntax error in rbt vcf-report.

[0.19.5] - 2021-03-05

Changed

  • Fixed internal file naming in order to avoid too long filenames.

[0.19.4] - 2021-03-04

Changed

  • Fixed further bugs in the csv-report.

[0.19.3] - 2021-03-02

Changed

  • Improved fasta sequence length retrieval in rbt vcf-report (@fxwiegand).
  • Better error messages (@fxwiegand).
  • Add check for empty values in rbt csv-report (@fxwiegand).
  • Removed unused dependencies (@fxwiegand).

[0.19.2] - 2021-02-12

Changed

  • Various small bug fixes in rbt vcf-report.

[0.19.1] - 2021-02-08

Changed

  • Fix for javascript import order problem in rbt vcf-report.

[0.19.0] - 2021-02-05

Added

  • New subcommand csv-report that allows to generate an interactive HTML report from a CSV/TSV table.

Changed

  • Some polishing for vcf-report.

[0.18.1] - 2021-01-27

Changed

  • If CANONICAL field is not present in ANN of bcf, rbt vcf-report now assumes that transcript is not the canonical one.

[0.18.0] - 2021-01-25

Added

  • Parameter --plot-info for rbt vcf-report that allows to plot arbitrary info fields next to the oncoprint matrix.
  • Ability to display intergenic variants at the primary stage of rbt vcf-report.

[0.17.0] - 2021-01-21

Changed

  • rbt collapse-reads-to-fragments now always writes FASTQ files since consensus reads need to be remapped anyways (MAPQ might change).
  • rbt vcf-report can now be parallelized.
  • Various fixes and improvements for rbt vcf-report
  • Various fixes for rbt collapse-reads-to-fragments

[0.16.0] - 2020-11-17

Changed

  • rbt collapse-reads-to-fragments bam writes skipped reads to separate bam file now
  • rbt collapse-reads-to-fragments bam does not perform starcode clustering anymore
  • Fixed bug in rbt collapse-reads-to-fragments bam failing when read mates map to different chromosomes

[0.15.1] - 2020-11-12

Changed

  • Fixed bug in vcf-split that led to unequally filled splitted VCF/BCFs.

[0.15.0] - 2020-11-11

Changed

  • Allow INFO field prefixes in vcf-report.
  • Require annotation with --hgvsg in vcf-report.
  • Fixes for vcf-report layout.

Added

  • New subcommand vcf-split for splitting VCF/BCF files into N equal chunks, including BND support.

[0.14.0] - 2020-10-26

Added

  • New flag --tsv for rbt vcf-report
  • --tsv allows adding a custom tsv file that will be visualized in the vcf-report

[0.13.0] - 2020-10-06

Changed

  • CLI syntax for rbt vcf-report has been changed in order to allow BCF/VCF files holding variants from multiple samples.

[0.12.2] - 2020-09-30

Added

  • New flags --info, --js and --format for rbt vcf-report
  • --js allows definition of a custom javascript template for creating vcf-reports
  • --info and --format allow specifying INFO- and FORMAT-fields that can be used by the custom javascript template

[0.12.1] - 2020-09-15

Added

  • rbt vcf-report allows to create an interactive HTML report allowing advanced analysis of variants from BCF/VCF and BAM files.

Removed

  • rbt oncoprint is now included in rbt vcf-report and therefore has been removed.

[0.11.0] - 2020-08-05

Added

  • Flag --sources that allows to constrain data sources for DGIdb annotation of VCF/BCFs.

[0.10.1] - 2020-05-13

Changed

  • Only print recurrent genes in oncoprint, in order to save time and space.

[0.10.0] - 2020-04-22

Added

  • rbt oncoprint, which allows to create an interactive HTML oncoprint from BCF/VCF files.

Changed

  • rbt call-consensus-reads has been renamed to rbt collapse-reads-to-fragments, which better highlights what is actually done.

[0.9.2] - 2020-03-20

Changed

  • BCF output for vcf-annotate-dgidb

[0.9.0] - 2020-01-12

Added

  • Subcommand rbt vcf-fix-iupac-alleles for converting IUPAC codes in VCF/BCF files into Ns.

[0.8.3] - 2019-11-08

Changed

  • Fixed a bug in annotate-dgidb where empty VCF input-files resulted in an error.

[0.8.0] - 2019-10-15

Added

  • Annotation of VCF/BCF files with drug interactions from DGIdb.

[0.6.0] - 2019-08-28

Added

  • Consensus reads can now be calculated from BAM files, based on marked PCR/optical duplicates from picard tools.

[0.5.0] - 2019-05-08

Changed

  • Fixed a bug in call-consensus-reads where read sequences were kept in memory. This significantly reduces memory footprint.
  • call-consensus-reads now writes shorter name lines for consensus reads. Name lines of consensus reads now only contain a random uuid and the number of reads they were created from. To get the old behavior, i.e. a list of reads that were merged into this consensus read, the --verbose-read-names flag can be used.

[0.4.1] - 2019-05-02

Changed

  • Fixed a bug in call-consensus-reads where BGZF-compressed files terminated early (after the first block).
  • Extended documentation of CLI.
  • Updated used versions of rust-htslib and rocksdb.
  • Renamed the --reverse-umi parameter of call-consensus-reads to --umi-on-reverse.

[0.4.0] - 2019-04-10

Changed

  • Consensus reads generated from UMI-tagged reads with call-consensus-reads no longer contain the UMI.

[0.3.0] - 2019-01-24

Added

  • A tool to merge FASTQ reads using unique molecular identifiers (UMIs).

[0.2.7] - 2018-12-28

Changed

  • Handle missing values in vcf-to-txt.
  • Bug fixes.

[0.2.6] - 2018-07-04

Added

  • Support for Number="R" tag in VCF files.

[0.2.5] - 2018-04-06

Changed

  • Fixed various small bugs.

[0.2.0] - 2018-02-23

Added

  • A tool to selectively remove records from a FASTQ file.
  • A tool to calculate b-allele frequencies (BAF) from a VCF file.

[0.1.3] - 2017-12-05

Changed

  • Adapted to changes in Rust-Htslib.

[0.1.2] - 2016-11-02

Changed

  • Improved robustness for exotic variant calls in vcf-match and vcf-to-txt.

[0.1.1] - 2016-08-31

Changed

  • Hotfix of a bug in vcf-match.

[0.1.0] - 2016-08-31

Added

  • Tool for matching VCF/BCF files.
  • Tool for converting VCF/BCF files to tabular TXT.
  • Tool for calculating BAM depth at given loci.
  • Tool for splitting FASTQ into n chunks in a single pass using a round-robin procedure.