v1.8.0

New Features

• cnvnator support
• breakseq vcf support

Improvements

• masking, dgv_annotation, and template_metadata files are now all optional
• Moved optional dependencies from the install_requires to tests_require and extras_require to improve setup
• Additional documentation and reorganization of the user manual
• Moved the complexity filtering to the summary stage

BugFixes

• Hard clipped read error during read alignment to contig
• vcf input option error where it was not being properly added to the supported tools

v1.7.1

Bug Fixes

• empty tab file error fix

Improvements

• set checker exit status
• improved error message on bad input directory for checker
• removed samtools as dependency (using only pysam now)

v1.5.3

Bug Fixes

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

v1.7.0

New Features

• convert option for the config command now accepts a variable number of input files to be converted
• sequence complexity filtering option
• Added mail options for slurm/sge

Improvements

• Added a more complex pipeline example to the documentation
• Added short contig assembly test
• Breakpoint distance pairing now accounts for untemplated sequence
• blat_rank has been renamed to alignment_rank and is now calculated for both bwa and blat
• alignment_rank is used to filter contig alignments so that there is only one contig alignment per contig
• Removed any unnecessary parameters
• checker is now detecting command not found errors
• filters spanning read alignments using the min contig score parameter (same filtering done on contigs)

BugFixes

• Filtering contig alignments was getting highest rank instead of lowest. Best ranks are lower ranks
• logs version for the configured aligner instead of just blat

v1.6.10

BugFix

• fixes error associated with drawing small exons at the start or end of a fusion transcript not being included in the interval mapping

v1.6.9

BugFixes:

• fixed interval error for single bp exon/insertion drawings

New Features

• small insertions/novel exons are now drawn taller than the surrounding exons
• small exons are not labelled and therefore not required to be the min object size
• added the new configurable drawing parameter exon_min_focus_size to determine a 'small' exon
• 'small' exons in the fusion transcript add the sequence to their labels

v1.6.8

BugFixes

• fixed annotations loading bug in auto-generating configs for transcriptomes libraries

v1.6.7

Minor BugFix

• config loading was not backwards compatible with older configs. Fixed so 1.6.6 can read configs from previous mavis versions as well

v1.6.6

New Features

• overlay read depth plot density

Improvements

• exon drawing, fixed overlapping exon issues
• additional columns to summary output
• additional metadata for pypi packaging

v1.6.4

BugFixes:

• #50 (minor) Was throwing an error that should be ignored when calling by flanking pairs