Cutesv

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

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

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

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.

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 |

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.