Mavis

BugFix
- 118: Bugfix files where the delimiter was missing from the header were being reported as empty instead of throwing an error

Bug Fixes

- Catches the empty file error thrown when no alignments are produced by blat

New Features
- Validation now drops breakpoint pairs with ranges outside the length of the chromosome they sit on allowing loading to continue past bad input events

New Features
- contig (or spanning-read) insertion calls are converted to duplication calls if more of the inserted sequence matches the reference sequence than is untemplated

Improvements
- BugFix: Summary step is no longer dropping single/ungrouped split read calls

New Features
- Added breakdancer support

Improvements
- speed-up improvements to both pairing and summary steps
- Fasta sequence ids for spliced predicted fusion products are now named using an md5sum hash of the sequence so that comparison during later steps does not require loading the fasta files
- Insertions called by are now being converted to duplications where appropriate

- Release includes speed-up improvements to both pairing and summary steps
- Fasta sequence ids for spliced predicted fusion products are now named using an md5sum hash of the sequence