Nanovar

Latest version: v1.6.2

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1.6.2

* Fixed bug where some supplementary alignments do not have primary alignments, in the case of a subsample BAM input

1.6.1

* Fix Tensorflow 2.16 compatibility issue, restrict tensorflow-cpu<=2.15.1 in setup.py

1.6.0

* Added NanoINSight INS annotation function (--annotate_ins [species])
* Fixed NanoVar report scatter plot xaxis range
* Changed Python version requirement to >=3.8
* Changed Biopython package version requirement to >=1.82
* Added full usage in README.md
* Added NanoINSight info in README.md
* Modified installation options in README.md

1.5.1

* BND SVs are now represented as one entry in VCF
* BND SVs now has an additional INFO attribute, CHR2, that records second chromosome name of BND
* Fixed cytocad import bug
* Fixed intersect_debug bug
* Fixed SVLEN float value bug
* Fixed missing FASTA entries bug

1.5.0

* Fixed font warning during report generation
* NanoVar no longer relies on HS-BLASTn (This would fixed multiple run errors)
* Suppressed keras tensorflow model warning
* Fixed nv_detect_algo import error due to Cython 3.0.2 Namespace update
* Reworked DUP calling to increase accuracy (Previously INS miscalled as DUP)
* Added MAPQ score filter against alignments between with 0 < MAPQ < 30
* HTML report is now a standalone file
* ins_seq.fa is output by default, it contains the inserted sequences of all INS SVs
* Removed ">" in SVLEN for one-sided INS SVs
* Temporary removed option to run CNV through CopyCAD (work in progress)
* Removed progress spinner and modified stdout status reporting
* Output no longer produces total.vcf file, unless --debug specified
* genome.sizes removed from output
* Modified paired INV breakends size calculation to that of single INV breakend (coord2-coord1)
* INS size adjusted (Taking median INS size across reads, instead of largest size)
* Simplified run status verbose
* Changed SVLEN placeholder for translocations and transpositions from '.' to 0.
* Changed translocation abbreviation from TLO to TRA
* Modified clustering from mean to median SV coordinates amongst reads
* Added NanoVar execution command into VCF header
* Included svtype in clustering filter
* Improved DUP calling by sequence mapping
* Improved SV genotyping
* Improved phasing of SVs sharing the same coordinates

1.4.1

* Bump version for Bioconda build for various Python versions

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