breseq v0.39.0

Version 0.39.0

• Fixed MAJOR ERRORS in assigning mutations to promoter regions of genes (#374)
• We are migrating the breseq documentation to the GitHub wiki. Please check there
  for the most updated version. The docs packaged with breseq are sunsetting.
• Commands like breseq BAM2COV and BAM2ALN are now more forgiving in the ways regions can be specified.
  • You can include commas in positions, which will be removed. REL606:627,165-627,185 orREL606:627165-627185
  • You can provide just a single position REL606:627165 or REL606:627165-627165
  • Hyphen-like characters (–) are automatically converted to hyphens (-).
• Removed an extra comma in gdtools COMPARE table output header (#368)

MacOSX binary updated on 10-22-24 to fix libz linking error (#386).

breseq v0.38.3

Version 0.38.3

• Miscellanous bug fixes related to nonstandard reference file loading.
• Fixed problem adding --isescan-results with Genbank input to breseq CONVERT-REFERENCE.
• Some commands (breseq BAM2ALN, breseq BAM2COV) will now create output directories if they don't already exist.
• Breseq now allows plus (+) and minus (−) signs to be used in reference seq ids, in addition to underscores and hyphens.
• Changed syntax for experimental breseq SOFT-CLIPPING command to allow multiple BAM inputs.

breseq v0.38.2

• Miscellanous bug files and updates to reference file handling.
• Updates to reference format documentation to describe how to get better IS prediction.
• Added experimental breseq SOFT-CLIPPING subcommand.

breseq v0.38.1

Very Minor Update

• Fix for infinite loop triggered by help when terminal window was too narrow.

breseq v0.38.0

• breseq can now analyze long-read sequencing data. It will split long reads into short subsequence reads that are of a length that works for its read mapping parameters and new junction analysis. Read splitting can be controlled with the --long-read-* options. If you are looking for structural variation, you should be performing de novo assembly and genome comparisons using other tools! breseq will not be able to identify or fully resolve large or complex structural variants.
• If you are using the current generation of Nanopore long read data, we recommend using the --nanopore option, which sets read mapping parameters that speed up the analysis and filters out predictions in error-prone homopolymer repeats of 4 or more bases.
• The MacOSX executable is now universal (should run on both Intel and M1 macs).
• Changed how reads that map equally to the reference and new junction get resolved to eliminate junctions that could get assigned high frequencies due to very little evidence, particularly in polymorphism mode. This approach is more conservative and may decrease the predicted frequencies of junctions, but should only have minor effects in consensus mode.

breseq v0.37.1

• Fixed bug in the way that indels in homopolymers were realigned for consistency that sporadically caused fatal "Covariate 'quality' exceeded enforced maximum" errors.
• Fixed fatal "Attempt to add duplicate of this existing entry" error that could arise when using user evidence Genome Diff files merged from outputs of previous runs.

breseq v0.37.0

• Warns that breseq results can vary (usually only slightly) with different bowtie2 versions and recommends a specific version for consistency.
• Added back code for shifting indels to improve mutation calling.
• Added an option for gdtools APPLY to output a new GD file showing the positions of each mutation in the (mutated) output genome.
• Updated documentation related to installation and explaining junction orientations.
• Fixed crash that could occur if there was a deletion spanning the origin of a circular reference sequence.

breseq v0.36.1

• Added an appendix to the manual describing how reference sequence files are loaded/used.
• When loading GenBank files that have a LOCUS line and source feature with different
  lengths, the LOCUS line length is now used to improve compatibility with sequences
  that have been edited in programs that do not update the source feature.
• Added a warning when CDS features with lengths that are not a multiple of 3 are loaded
  with a suggestion to change these to pseudogenes. Changed a fatal error when annotating a
  mutation in an incomplete final codon in one of these CDS features to a warning and generic coding mutation.
• breseq will no longer throw a fatal error if read files that have the same name
  but are located at different paths are input.
• Fixed gdtools MERGE not preserving header information from first GD file.
• Fixed treatment of UNDEFINED by gdtools FILTER/REMOVE to allow matches to != UNDEFINED.

breseq v0.36.0

• Fixed an issue causing JC evidence to not save info in annotated GD files.
• Fixed a crash when annotating GD files containing INV mutations.
• Fixed empty line at the end of the FASTQ input causing an error.
• Major updates to gdtools commands.
• gdtools COMPARE/ANNOTATE
  • New TABLE format that provides a text (CSV) version of HTML style compare table.
  • TEXT_* output columns added if -b option provided.
  • Changed HTML default to not repeat header lines for easier loading into Excel.
    If you liked these, you can add them back as before with --repeat-header 10.
• gdtools FILTER/REMOVE
  • Added the ability to preserve evidence entries.
  • Added control over commenting/removing filtered lines, renumbering IDs, and verbose messages.
  • Fixed (and explained) logic for matching the UNDEFINED value
  • New ASSIGNED field for filtering on whether evidence is used.
  • Added some examples of usage to the command line help.

breseq v0.35.7

• Speedup and fix of rare bug related to annotating mutations to properly account for cases in which multiple base substitutions occur in the same codon.