Nanovar

Latest version: v1.8.1

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1.2.4

* Replaced keras with tf.keras (>=2.0.0) to avoid compatibility errors
* Fixed progress spinner overflow by adding boolean

1.2.3

* Fixed progress spinner by increasing sleep time

1.2.2

* Updated dependency versions
* Changed spline in nv_cov_upper to make_interp_spline due to scipy update

1.2.1

* Added running progress spinner
* Added bedtools as a pre-requisite for pybedtools
* Added installation of dependencies if using conda
* Updated MANIFEST.in
* Updated README.md, added badges
* Tested in Python 3.5, 3.6, 3.7

1.2alpha

* Program language migration to entirely Python 3.7
* Distributed as a python PyPI package and a conda package
* Added requirements of Blast binaries from NCBI-BLAST Version 2.3.0+ and HS-BLASTN v0.0.5+
* Added new parameters: --minalign, --buffer, --force
* Changed input FASTQ/FASTA, reference genome and working directory to positional arguments
* Changed default minimum SV len to 25 bp
* Removed short-read support and bowtie2 requirements
* Improved VCF file formating
* Added FORMAT column
* Added genotype, read-depth and allele read-depth information
* For BND SV type, ALT coloumn now shows a breakend record as specified in VCFv4.2
* For BND SV type, INFO field "SV2" is added to indicate translocation (TLO) or transposition (TPO)
* Changed INFO field naming: LCOV to SR, PROB to NN
* Removed INFO fields: SCOV, SVRATIO
* SV len is now estimated for tandem duplications
* FILTER column now shows "PASS" if SV score above/equal to score threshold, or "FAIL" if SV score below score threshold
* Replaced read_name in each SV ID with an arbituary SV number

1.1.1

* Added gcc, ldd library requirements
* Added Tensorflow installation check

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