Nanovar

* 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

* 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

* 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

* Bump version for Bioconda build for various Python versions

* Implemented a large cytogenetic variation detection algorithm through CytoCAD (Add the paramenter "--cnv hg38" during run)
* Added LINE (L1) and SINE (Alu) novel insertion detection functionality (NanoVar screens the sequence of INS SVs
for L1 and Alu elements and output the results in the INFO column of VCF file (E.g. TE=L1HS)
* Updated curated hg38 filter file (added all N regions)
* Expanded the CIGAR reading values to include '=' and 'X'
* Improved breakpoint clustering algorithm and rectified bugs
* Modified setup.py to state compatibility with python3.8
* Fixed Numpy VisibleDeprecationWarning in nv_report.py
* Added '--pickle' arguement for debugging purposes (Hidden option)
* Added '--archivefasta' arguement for debugging purposes (Hidden option)
* Added '--blastout' arguement for debugging purposes (Hidden option)

* Fixed nv_detect_algo insertion and deletion large size bug
* Added pysam >=0.15.3 into bioconda metal.yml as prerequisite
* Added pybedtools >=0.8.2 prerequisite to fixed RuntimeWarning buffering=1 error (Refer to https://github.com/daler/pybedtools/issues/322)
* Prevent repeated read-indexes by adjusting seed (Thanks to Geoffrey Woodland)
* Improve read cluster exception message (Thanks to Geoffrey Woodland)
* Unique ID of breakpoints identified by BLAST shortened to four characters to prevent mixing with minimap2 breakpoints
* Adjusted breakend filtering during mm clustering
* Improved breakpoint clustering algorithm to increase accuracy
* Added newline to last line of genome.sizes file
* Added genome check for BAM (Thanks to oneillkza, https://github.com/cytham/nanovar/issues/19#issuecomment-791599629)
* Modified argparse "usage" format
* Suppressed BAM index missing warning
* Supressed Tensorflow INFO and WARNING logs
* Migrated to tensorflow-cpu/tensorflow-mkl to prevent cuda_driver.cc error
* Fixed FixedLocator warning