NanoVar Changelog


Release Summary:


Version 1.2.4 - Nov 25, 2019
    * Replaced keras with tf.keras (>=2.0.0) to avoid compatibility errors
    * Fixed progress spinner overflow by adding boolean


Version 1.2.3 - Nov 25, 2019
    * Fixed progress spinner by increasing sleep time


Version 1.2.2 - Nov 25, 2019
    * Updated dependency versions
    * Changed spline in nv_cov_upper to make_interp_spline due to scipy update


Version 1.2.1 - Nov 24, 2019
    * 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


Version 1.2-alpha - Nov 21, 2019
    * 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


Version 1.1.1 - Aug 29, 2019 [Archieved]
    * Added gcc, ldd library requirements
    * Added Tensorflow installation check


Version 1.1.0 - June 23, 2019 [Archieved]
    * Migration from Python 2 to Python 3


Version 1.0.1 - June 21, 2019 [Archieved]
    * Fixed chromsome naming bug
    * Fixed python pip installation of updated packages


Version 1.0 - May 12, 2019 [Archieved]
    * Initial release
