breseq v0.35.6

• Fixed compatibility with GenBank reference files produced by Prokka and NCBI PGAP, and with GFF3 files produced by PGAP.

breseq v0.35.5

• Bug fix for incorrect "Plots could not be created" message in HTML pages when -j is >1.
• Bug fix for #254: "Provided translation table #0 does not have 64 codons". This was a rare
  case where two SNPs occur in the same codon of a CDS and also overlap a noncoding gene.

breseq v0.35.4

• Critical bug fix for crashes during output creation when -j is >1

breseq v0.35.3

• Fixed problem where HTML coverage and alignment files were not produced. (Bug introduced in v0.35.2)
• Fixed overlap and annotation position problems applying INT mutations with length zero.
• Added -seq-id|-s option to gdtools APPLY so that one can remove extra reference sequences that
  were only provided for INT, CON, MOB, etc. mutations before output.

breseq v0.35.2

IMPORTANT: This release has a KNOWN ISSUE. It does not correctly generate HTML output files.

Please update to v 0.35.3 or later!

• Generation of output files is now multithreaded.
• Changed --use-version-as-seq-id option to --genbank-field-for-seq-id to give more control over
  choosing which part of the header is used for the sequence ID. The default is to assign to the
  first existing field with the preference: LOCUS > ACCESSION > VERSION.
• Fixed GenBank parsing to be more forgiving of different LOCUS lines output by other programs.
  Now only gives a warning if the sequence length is missing and looks for the linear|circular
  designation at different locations within the LOCUS line. Falls back to the source feature
  length if the sequence length is missing from the LOCUS line.
• Changed priority of name used for features in GenBank files to name > gene > locus_tag > label > note.
• Added mutation type INT for applying GenomeDiffs to insert a sequence with annotations.
• Fixed multiple identical GD entry error related to --user-evidence leading to
  double mutation predictions.
• Changed error from loading reference genome files with repeat regions annotated
  with complex/multiple locations to a more informative warning.
• Fixed major memory leak during the output step related to assigning read counts to
  JC evidence from BAM files. Rewrote to further improve performance by making access
  to the required files for this step persistent.
• Added summary.json and output.vcf to the output directory (they are also present in the data directory).
• Fixed --total-only mode for breseq BAM2COV to give expected output in --table mode.

breseq v0.35.1

• Fixed bug introduced in v0.35.0 that resulted in displaying an error message that
  "Coverage plot could not be generated" instead of the plot on MC evidence pages.
• Added missing input file 'empty.fastq' needed for ./run_tests.sh.
• Added FASTA output option to gdtools COMPARE/ANNOTATE. This will generate a
  multi-FASTA file with a genotype alignment suitable for building phylogenetic
  trees using parsimony methods. The content is equivalent to that of the PHYLIP
  output option, but without the length limitation on the genome names.
• Added --user-version-as-seq-id option to breseq. If present, it will use the full
  VERSION in an input GenBank file (e.g., NC_001416.1) as the sequence ID instead of
  the LOCUS (e.g., NC_001416). You will need to use the converted reference file
  (data/reference.gff) for further breseq and gdtools operations on breseq output
  generated using this option.
• While not generally recommended, using read and reference file names and output paths
  that contain spaces in them should now work.
• Fixed bug in gdtools ANNOTATE that caused it to fail with --preserve-evidence.
• Miscellaneous improvements to other gdtools subcommands.

breseq v0.35.0

• Increased specificity of JC prediction. Reads are now only assigned to candidate
  junctions that are their best matches. They are never assigned to other junctions,
  even if they match them better than the reference. To get the earlier behavior
  (which might be preferred for consensus mode or for predicting polymorphisms from
  a population with little diversity use the --junction-allow-suboptimal-matches option.
  This option can result in some reads being misassigned to the wrong junctions.
• Fixed various errors when using --user-evidence files and --aligned-sam input.

breseq v0.34.1

• Fixed bug that predicted zero-length deletions in circular genomes.
• Fixed bug that caused runs to fail when an empty read file was provided as input.
• Fixed predict mutations junction side_1_position > side_2_position bug.
• Added pipeline control options (--skip-*-prediction). Implementation is still experimental.

breseq v0.34.0

• Fixed bug where two rejected JC evidence items could predict a mutation.
• Added new option --junction-minimum-pr-no-read-start-per-position to prevent saturation
  of coverage in high-coverage samples from leading to rejection of valid JC prediction.
  Set this option to 0.0 if you want to use the behavior of previous versions.
• Changed default for --consensus-frequency-cutoff to be 0.8 in polymorphism mode,
  instead of 0.0, to prevent accepting rejected polymorphism RA items as consensus predictions.
• Added the ability to predict DEL spanning the origin of a circular reference sequence.
• Changed plotting scripts to be more compatible with fonts available to different versions of R.
• Miscellaneous fixes to make gdtools commands more robust.

breseq v0.33.2

• Fixed extremely rare fatal error in constructing junction sequences with overlap
  that ended at the boundaries of reference sequences.
• Multiple gdtools COMPARE updates. Fixed bug leading to empty PHYLIP output and
  restored sorting of columns in HTML output based on GenomeDiff metadata.