syri v1.7.0

• Updated installer to use pip (instead of setuptools)
• Cleaned import commands to work better with newer versions of cython
• Updated log commands
• Updated code to fix pandas warnings
• Fixed typos in VCF output header

syri v1.6.3

• Syri can now also print sequence for large indels
• Added parameter to toggle HDR printing
• Added parameter to control max size for INDEL/HDR sequence printing
• Improved logging
• Bug fixes

SyRI v1.6

• Added --invgaplen parameter to regulate the gap length between alignments of an inversion. This can also be used to filter out inversions with very different sizes between the reference and query genomes
• Added reader for PAF files and can be used using -F P
• Update README

Testing conda v1.5.3

Rearranged files and folder and setup conda recipe

SyRI v1.5.1

• Bug fix
• Removed use of depreciated numpy type usage

SyRI v1.5

• Updated for python >=3.8
• Removed biopython as dependency
• Plotsr is packaged as a separate package and is not part of syri bins now.

SyRI v1.4

• Added --tdmaxolp to limit the max overlap between two translocations.
• Added -f parameter to trigger automatic filtering of low quality alignments. Now, by default, SyRI only uses alignments with alignment identity > 0.9 and alignment length > 100.
• Added samtocoords to parse alignments from SAM file into a coords table.
• Chroder now uses the longestrunsubsequence package to improve performance. This will improve performance in worst-case scenarios where earlier, chroder would get stuck consuming large amount of memory.
• Plotsr now provides a list of plotting backends for selection. This would help in cases where the default backend is not available.
• Minor bug fixes, code improvements, and clean-up.

SyRI v1.3

• Improved translocation and duplication identification performance. For this, SyRI now uses new heuristic which limits how candidate translocations and duplications are selected. The heuristic uses a new parameter tdgaplen which limits the maximum gap-length between the alignments of a candidate TD. This should not have any major effect on the biologically meaningful TDs.
• Added a new script plotsr that uses SyRI's output and generates a plot depicting syntenic and rearranged regions in the homologous genomes.
• SyRI now also generates a summary file describing the count and length of genomic annotations.

SyRI v1.2

Improved performance for inversion identification. Added more informative error messages. And bug fixes.

SyRI v1.1

Improved performance for translocation and duplication identification. Bug fixes. Removed the unused -o parameter from SyRI (file names are controlled using the --prefix parameter).