Version update

1. fix bugs in resolving reference genomes
2. modify several dependencies and remove some useless dependencies
3. update several evaluation scripts

Version update

1. Speed up both SV discovery calling and force calling comprehensively.
2. Upgrade the force-calling module.
3. Update several functions and regulations.

Version update

1. Fix the error of missing min_size parameter.
2. Fix the missing signatures in duplication clustering.

Version update

1. Fix several errors in signature extraction.
2. Filter low quality reads in the statistics of reference reads.
3. Modify the rule of merging signatures on the same read.
4. Modify the cluster rule of insertions and deletions in force calling.

Version update

1. Fix an error in handling strand in force calling.
2. Speed up the genotype module of discovery calling. The comparison results on various datasets are as follows.

	cuteSV (previous)	cuteSV2 (latest)
CCS	900.37s	261.77s
CLR	3620.00s	2644.94s
ONT	2893.08s	1264.26s

Version upgrade

cuteSV (v2.0.0):

1. Upgrade the force-calling module.
2. Add --remain_reads_ratio parameter in order to generate a highly accurate record by discarding a few signatures.
3. Fix several bugs in inversion and translocation calling.
4. Remove the redundant operations in the signature extraction and accelerate the whole analysis.
5. Streamline the translocation output when performing force-calling.
6. Modify the signature matching rule.
7. Modify the sequence of the inserted allele.

v1.0.13

1. Modify the breakpoints of alternative allele and reference allele.
2. Fix an initialization error that will reproduce wrong diploid-assembly-based SV call.

v1.0.12

cuteSV (v1.0.12):

1. Add Allele frequency (AF) info in the outputs.
2. Fix an index error when force calling BND variants.
3. Modify the parameter of --max_size and enable to report full length of SVs.

cuteSV-v1.0.11

cutesv (v1.0.11):

1. Add a script for post-processing typically cuteSV callsets from assembly-based alignments to generate the diploid-assembly-based SV calls.
2. Give a wiki page for helping uses to achieve assembly-based SV calling.
3. Improve acquirement of inserted sequence in a read whose primary alignment contains hardclips.
4. Improve the performance of force calling.
5. Enable cuteSV to output allele sequences when performing force calling with the VCF generated from other callers.
6. Fix bugs to avoid the error raised by abnormal SV type.
7. Update the sort commands used in cuteSV.
8. Update the parameter of --max_split_parts.

cuteSV-v1.0.10

cutesv (v1.0.10):

1. Fix a bug leading to calculate wrong TRA positions.
2. Add a file format conversion script that enable to transfer the vcf file to bedpe file.
3. Involve several clustering-and-refinement strategies in force calling function.
4. Assessed the performance of force calling with Giab HG002 sample datasets (including CLR, CCS, and ONT platforms).