NanoVar Changelog


Release Summary:


Version 1.3.4 - Mar 19, 2020
    * Fixed missing nanovar script


Version 1.3.3 - Mar 19, 2020
    * Upgraded model (ONT (Guppy) - v1, pacbio (CLR or CSS) - v1)
    * Modified normal read breakpoint buffer from 400 to 100 to include shorter alignments as breakend-opposing reads
    * Survey invalid symbols in contig ids and ignore reads mapping to these contigs (Thanks to Simone, https://github.com/cytham/nanovar/issues/6#issuecomment-595851018)
    * Added a new debug file 'detect.tsv'
    * Removed blast table intermediate file when not debugging
    * Added limitation section in README.md


Version 1.3.2 - Mar 4, 2020
    * Fixed VCF header unclosed quotes (Thanks to Scott, https://github.com/cytham/nanovar/issues/5#issuecomment-592961341)
    * Improved clustering algorithm (Clustering left and right breakends of each SV separately)
    * Updated README.md


Version 1.3.1 - Feb 29, 2020
    * Fixed cython compilation bug (Thanks to Scott, https://github.com/cytham/nanovar/issues/5#issuecomment-592766203)
    * Updated requirements.txt


Version 1.3.0 - Feb 28, 2020
    * Tool requirement changes:
        * Added SAMTools
        * Added Minimap2

    * Algorithm and pipeline changes:
        * NanoVar now uses both minimap2 and hs-blastn for increased sensitivity
        * Upgraded model (v5)
        * Improved time complexity for clustering algorithm
        * Minor tuning of SV confidence scores by normal read coverage and number of alignments
        * Default SV read support -c changed from 1 to 2
        * Added progress information command-line feed during the run.

    * Input/Ouput changes:
        * NanoVar can now take a BAM file (tested BAM from minimap2) as input instead of FASTQ/FASTA reads
        * Added ONT/PacBio option (For future use, currently both tech uses same model)
        * Added custom model option
        * Added --debug option
        * Added Minimap2 executable path option
        * Added SAMTools executable path option

    * VCF format changes:
        * "END" coordinate for BND SVs will now show POS+1 coordinate instead of "." to be usable for IGV (Thanks to Scott,
        https://github.com/cytham/nanovar/issues/5#issue-559151039)



Version 1.2.7 - Dec 15, 2019
    * Upgraded model (v4)
    * Changed default score threshold to 1.0
    * Added --mincov argument
    * Added genotype prediction thresholds --homo --hetero
    * Fixed make_interp_spline bug (Thanks to Asma, https://github.com/cytham/nanovar/issues/1#issue-536971382)
    * Fixed logging oversize
    * Fixed HTML figures and file path link
    * Disabled sorting by bitscore


Version 1.2.6 - Nov 28, 2019
    * Fixed svread-overlap.tsv file formating in nv_nn.py
    * Fixed operation bug in nv_valid.py l201


Version 1.2.5 - Nov 25, 2019
    * Python 3.5 is no longer supported


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
