Skip to content

CHANGELOG.md

Latest commit

 

History

History
89 lines (53 loc) · 3.96 KB

CHANGELOG.md

File metadata and controls

89 lines (53 loc) · 3.96 KB
Raw

CHANGELOG

1.4.0

  • fix: properly parse args by revering global structopt setting from @chenrui333

1.3.0

  • fix: typo in count_mate_resolutions from @camlloyd
  • chore: added CONTRIBUTING.md per @mbhall88 suggestion
  • fix: handle missing ref files gracefully
  • fix: many small typos, improved help messages, fixed conflicting short opts

1.2.0

  • Fix: Handle BAM records with empty SEQ fields (* in SAM format) in base-depth. Previously this would cause an out-of-bounds error. Now these reads still count toward depth, and their bases are counted as N. (#92 by @ghuls)
  • Chore: Update deps and fixup lints

1.1.0

  • Fix/Feat: For both MapQualBaseQualN and BaseQualMapQualN only resolve to N when the bases are ambiguous, otherwise return the consensus base.

1.0.0

  • Feat: expand mate-fix resolution strategies
    • Adds new output columns for IUPAC bases, which are only used for some of the mate-fix resolution strats
    • By default the "original" mate fix strat will be used and remains backward compatible

0.10.3

  • Bugfix: Fixed mate selection in --mate-fix to correctly prefer first mate over second mate when MAPQ scores are equal (issue #82)

0.8.3

  • Updated dependencies - to fixed version of gzp

0.8.2

  • Updated dependencies

0.8.1

  • Bugfix --keep-zeros and --no-merge had an incorrect conditional resulting in all positions being filtered out.

0.8.0

  • Added --keep-zeros option to prevent truncating regions that have 0 depth at the start / end of the interval
  • Added --skip-merging-intervals to prevent the merging of overlapping intervals if a BED/VCF/BCF file is used to specify regions. This will produce duplicate entries
  • Improved error message for invalid BED file
  • Improved handling of 3-column BED files (they now work)
  • Moved to gzp for multithreaded BGZF output writing when specified. Also added compression-threads and compression-level options
  • Updated all deps

0.7.4

  • Add --bed-format flag to only-depth to output a bed-like file with the depth in the 5th column and no headers.

0.7.3

  • Update all dependencies, specifically htslib to hopefully sort out openssl errors in the conda build process.

0.7.2

  • Use published version of noodles so we can publish on crates.io

0.7.1

  • Fix regression in release profile

0.7.0

  • Added --min-base-quality/-Q flag to the base-depth tool. When present, this flag will cause a base quality check of reach base. If the quality is less thn the specified minium quality the depth will be counted as an N instead of an [A, C, T, G]. If this flag is not set the behavior is not changed.
  • Added the --bgzip/-Z flag to all subcommands which bgzips the output. Note that this does not index the bgzipped file at this time. This can still be done with tabix -S 1 -s 1 -b 2 -e 2 ./output.tsv.gz
  • Changed log level of "Batch Processing ...", "Processing ...", and "Processing region" logging statements to trace. Set RUST_LOG=trace environment variable to restore previous logging verbosity.
  • Added "Processing TID ..." log statement at info level (on by default).
  • All perbase commands now gracefully handle broken pipes and exit 0.

0.10.0

  • fix from @biermanr for 71 (--keep-zeros skip/dup loci)

0.10.1

  • fix from @nkkarpov updates smartstring version wich fixes some UB in old smartstring.

0.10.2

  • fix Update htslib version v0.39 by @davidecarlson