breseq v0.28.1

• Fixed R out-of-range integer error encountered when one of the reference sequences had very high read-depth coverage.
• Extra validation steps for Genome Diff files with complex mutational series (using 'within' and 'before' fields) may require updates (corrections) for manually edited Genome Diff files when they are used with certain gdtools commands.

breseq v0.28.0

• Revamped how gene locations are handled internally to deal with complicated cases: trans-spliced genes, internal frameshifts, indeterminate start/end coordinated found in incomplete genomes, genes that cross the origin of circular chromosomes, etc.
• Optimizations to improve slow fitting of very high coverage reference sequences, and for junction predictions involving these sequences (for example, in samples containing high copy number plasmids).
• Various fixes for gdtools commands.

breseq v0.27.2

• breseq CL-TABULATE command for analyzing changes in contingency loci (hypermutable homopolymer stretches).
• Bug fixes and updates to various gdtools and breseq utility commands.
• Fixed rare bug leading to duplicate mutation predictions in repeat regions.

breseq v0.27.1

• Improved stability; fixed two sources of rare crashes.
• The samtools executable is no longer included/installed/required.
• Fixed backward compatibility with RA lines that was broken in 0.27.0

breseq v0.27.0

• Now accepts gzipped (*.gz) FASTQ input files.
• Logic and options controlling predictions of consensus versus polymorphic
  mutations improved and now explained via flowcharts in the documentation.
• Three new tutorials from EMBO course added to the documentation.
• Continued updates and improvements to various gdtools commands.

breseq v0.26.1

• Fixed a crash that sometimes occurred when processing polymorphism statistics.
• Corrected handling of shifted positions for some indel mutations.
• Updates to several gdtools commands. Usage changed in some cases.

breseq v0.26.0

• First version with binary distributions for Linux and MacOSX.
• Updated HTML documentation (installation instructions, annotated bibliography, FAQ).