basevar v1.2.0

Version 1.2.0

Update:

• bugs fix.
• using the source codes of @htslib/c705bec (20241216) directly instead of using as a submodule
• modify htslib/Makefile and fix compilation bugs

basevar v1.1.2

Version 1.1.0

Update:

• bugs fix.

basevar v1.1.0

Version 1.1.0

Update:

• add a module to concat VCF/CVG files that generated by BaseVar
• performance improvement
• fix the known bugs

basevar v1.0.0

Release the first C++ version of BaseVar

This is the first official version of BaseVar that has been fully implemented by C++. This version delivers a computing speed exceeding 20 times that of the Python version, all while demanding substantially less memory.

• Use C++ to improve the performance of BaseVar;
• Rewrite the whole codes and functions;
• Use htslib to deal with BAM/VCF/CVG files
• Make buffer for samples's BAM in specific genome regions, this could improve the performance;
• Fix some bugs.

basevar v0.8.0

This version has more than 10 times performance improvement than the preview version.

• Use cython to improve the performance of BaseVar;
• Use htslib instead of pysam. Now I give up pysam in BaseVar;
• Make buffer for samples's BAM in specific genome regions, this could improve the performance;
• Rewrite many codes and many functions;
• Make smart-rerun much smarter;
• give up Numpy in variant caller functions;
• Use htslib for bgzip and tabix.
• Fix some bugs.

basevar v0.6.1.1

fix the bug in scan_indel function