Minor enhancements

• Report SVLEN in output VCF for insertions
• Report all GFF fields in output VCF
• Ability to generate breakpoint library FASTA in BreakSeq 1.0 format
• Tolerate missing insertion sequence file (.ins) when building bplib FASTA
• Only generate FASTA sequences around junctions for specified chromosomes

Minor updates and bugfixes

• Perform only the required processing to report SVs on specified chromosomes
• More checks, balances, timing and logging

Initial release of BreakSeq2

• Builds up on BreakSeq to use all read alignments for significantly improved sensitivity.
• Supports breakpoint libraries as FASTA or GFF. In case of GFF, the FASTA version is generated and used for alignment using BWA. The junction library generation is also parametrized to support longer reads.
• Improved logging and error reporting.
• Easy install process using the Python installer pip