breseq v0.33.1

• CRITICAL bug fix for a crash during the final output step when there are
  large deletions overlapping a single gene.
• Positions of indel mutations are no longer normalized in polymorphism mode
  because this process can fail and lead to duplicate GD entries. Note: you can
  still use gdtools NORMALIZE on a GD file output by a polymorphism mode run if you
  want to compare it to GD files from consensus mode. Just be aware that NORMALIZE
  may fail if you have certain complicated cases with multiple base substitutions
  and indels near one another such that shifting them can lead to conflicts.
• Added option to preserve evidence entries to gdtools ANNOTATE.

breseq v0.33.0

• Changed behavior of gdtools SUBTRACT to ignore mutation frequencies by default;
  and fixed floating point error when frequencies are taken into account
• Separated output of normal annotation of mutations in a GD file and
  additional HTML-specific fields. gdtools ANNOTATE/COMPARE has a new option to
  add the supplementary html_* and position_start/end fields if you need them.
• Changed character separating annotation information about multiple overlapping
  genes to '|' from ';'.
• Improved automatic detection of libunwind and added configure option (--without-libunwind).
  Changed default settings to not use libunwind for binary builds to improve compatibility.

breseq v0.32.1

• Added --minimum-mapping-quality option. Currently it is OFF by default.
• Fixed incorrect ordering of read mapping criteria that could lead to longer but worse alignment
  being accepted over shorter match that did not meet --required-match-fraction
• Removed the gdtools MERGE subcommand (it had become equivalent to gdtools UNION).
• Fixed adding correct gene features to copies created by AMP mutations in gdtools APPLY.

breseq v0.32.0

• If a mutation overlaps multiple genes, its effect on each gene is now annotated.
  (Previously only the first gene encountered was annotated.) The relevant Genome Diff
  fields use a semicolon to separate the information about each impacted gene.
• New output of summary information and settings in JSON format in data directory file
  summary.json.
• Corrected case in polymorphism mode where failing consensus mutations could be
  incorrectly predicted if a polymorphism was rejected. More thorough and consistent
  output of rejection information for RA evidence.
• Updates to VCF output.
• Fixed problem reading some FASTQ files (discovered on Nanopore data).
• More granular options to filter predictions on the coverage of reads supporting them.
  For example:
  --polymorphism-minimum-variant-coverage
--polymorphism-minimum-total-coverage
--polymorphism-minimum-variant-coverage-each-strand
--polymorphism-minimum-total-coverage-each-strand
  WARNING: Previous versions of these options have been renamed for consistency.
• New options to customize bowtie2 options used for alignment. (Only intended for expert users!)
  --bowtie2-scoring, --bowtie2-stage1, --bowtie2-stage2, --bowtie2-junction
• Removed extra slash in paths to invoke R scripts.
• Removed split alignment pieces that were completely soft-padded in output BAM file.
• C++11 is now required for compilation. Optimization added to default compiler settings.
• Fixed compatibility issues when compiling with certain versions of GCC.

breseq v0.31.1

• Critical fix for checking new bowtie2 versions with extra decimal place (e.g., 2.3.3.1).
• Additional bug fixes for fitting coverage distribution.
• Fix for gdtools SUBTRACT when using both polymorphism and consensus inputs.

breseq v0.31.0

• Fixed critical error that could give negative positions for mutations when a reference sequence fragment was called as deleted.
• Fixed several cases where fitting coverage distribution could fail or lead to a fatal error.

breseq v0.30.2

• Improved robustness of fitting coverage distribution and added fallbacks if fitting fails.
• More information at the command line and on the HTML summary page about when insufficient coverage leads to an entire reference sequence being called as deleted and when predictions will be less reliable due to failure fitting the coverage distribution.
• More detailed debugging information output for errors and crashes.

breseq v0.30.1

• Command line options added to allow control over how reads are filtered.
• Reads with length ≤18 are now ignored by default to avoid problematic memory usage associated with how they can ambiguously match many different junction sequences.
• Fixed bugs related to duplicate INS/DEL mutations being predicted in polymorphism mode.
• Reports error if Bowtie2 version 2.3.1 is used. Upgrade to a newer Bowtie2 version.

breseq v0.30.0

• Options used in calls to bowtie2 were changed to be compatible with bowtie v2.3.0. These changes may result in (small) changes in how reads are aligned versus in older breseq versions.
• Fixed bug in polymorphism mode option --polymorphism-reject-surrounding-homopolymer-length and its default setting. This filter had been operating differently, and more stringently than intended, resulting in the rejection of certain polymorphisms when the same base as the variant base was present in the reference genome at positions immediately before and after the mutation.
• HTML and GD output now include a POLYMORPHISM_REJECT field describing why a putative polymorphism was reassigned as a consensus mutation with 100% frequency (i.e., rejected as a polymorphism).
• Fixed rare cases where certain GenomeDiff files output by breseq failed when they were used with gdtools APPLY.
• Fixed various bugs related to reference files containing nonstandard bases, spliced genes, and certain seq_id names.

breseq v0.29.0

• CRITICAL fixes for polymorphism mode bugs that could lead to missing high frequency
  mutations when compiled on certain platforms and in very high coverage samples.
• Updated included SAMtools version to 1.3.1; added multithreading to samtools sort steps.
• Other fixes to enable output from other mapping programs using --aligned-sam mode.
• Other minor bug fixes and improvements.