Changelogs » Mavis

Mavis

2.2.6

BugFixes

189 Fix clustering bug by shifting start of second breakpoint for intra-chromosomal breakpoint merges
195 BugFix from the 2.2.5 release where these were defaulted to strings instead of arrays

Features

Update readthedocs configuration
Add python3.7 to the tox and travis configs
Update the contributor directions

2.2.5

BugFixes

188 Allow numeric values for JSON annotations file strand values
Features

188 Add option to include non-coding transcripts in the annotations file

2.2.4

Bugfixes:

185 186 Fixing OpenBlas issue by explicitly setting the number of threads when numpy is imported.

2.2.3

Bugfixes

182 183 Fixing README.md so it can be converted to rst and displayed in PyPI nicely.

2.2.2

Bugfixes

179 Making the outputs more consistent across multiple runs.

2.2.1

Bugfixes

175 Adjusting qstat command so that the output is in the expected format

2.2.0

Improvements:

165 Adding reference and alt calculator as a utility script
171 Adding STAR-Fusion as a supported tool

2.1.7

Improvements:
* 167 Adding support for mouse mm10 cytoband information

2.1.6

Improvements

* Introduces Travis CI to the repository

Bugfixes

* 158 Fix issue to ignore reads that have unmapped mates when gathering flanking evidence.

2.1.4

BugFix
- Warn only on missing aligner instead of throwing error so that mavis can be used as a package dependency

2.1.3

BugFixes

* 151 Allow summary to collapse all events by distance if they are called the same way, not just events called by split reads

2.1.2

BugFixes

- support scheduler job time formats >1 day
- support ext hgvs variants
- breakpoint ordering for duplications within repeats

2.1.1

BugFixes
- Fixed minor drawing bug for very small genes with a single exon

Documentation
- Added citation information to README

2.1.0

Improvements
* Allow strelka indels to be a valid input to convert/config

bugfix
* 136 Fix issue where the path to the blat binary could not be found.

2.0.0

MAVIS 2.0.0 has similar underlying mechanics to its predecessors in how it validates and processes structural variants. However, significant improvements to how MAVIS interacts with the scheduler have been made. This should improve the user experience.

**New Features**
- MAVIS now uses pythons built-in logging module so that different levels of logging can be selected to help debugging if uses encounter issues.
- MAVIS can be run locally without a scheduler, instead setting up its own multiprocessing using pythons concurrent.futures library
- Increased integration with schedulers to automate submitting, resubmitting, and monitoring jobs
- Support for buildout. This allows the user to create a mavis binary rather than having to install MAVIS into an existing python. This will improve the process of setting up and integrating MAVIS into existing bioinformatic pipelines
- A second tutorial which uses a smaller dataset and can be run locally on the average personal computer has also been added. This will make it easier for users to evaluate their MAVIS install

**Improvements**
- Ignores and logs problem (invalidly formatted) reads, instead of throwing an error. This will allow users to proceed even when their BAM file may contain 'dirty' reads.

1.8.5

Improvements
- Ignores invalid reads where there is a cigar string but no aligned portion. Logs a warning

1.8.4

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

1.8.3

Improvements
- prints log errors when the validation step was run after annotations (a partial rerun)
- standardization of spanning read calls
- pairing states for transcriptome vs genome using either pairing type (pairing, inferred_pairing)

Bug Fixes
- reference files (with defaults set from environment variables) was still requiring the argument. Now the argument is optional when the default is present
- read evidence undercalled due to strand being set for unstranded sources
- explicit hashing of reads to avoid over-counting

1.8.2

Bugfixes
- Fix for loop during filtering low weight edges in assembly
- Fix for drawing consecutive exons spacing

Improvements
- Style fixes for stricter pycodestyle

1.8.1

Improvements
- Better error messages for config validation errors
- Set 0mq only for non-best blat alignments (even when multiple ties)
- merge data columns when collapsing bpps read from tools
- collect extra breakdancer columns
- greedy algorithm to remove fragment size outliers during call by flanking pairs to avoid coverage too large errors and allow more calls

1.8.0

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

1.7.1

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)

1.7.0

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

1.6.10

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

1.6.9

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

1.6.8

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

1.6.7

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

1.6.6

New Features
- overlay read depth plot density

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

1.5.4

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

1.5.3

Bug Fixes

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