Cutesv

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

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.

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.

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).

1. Change 0-based pos into 1-based pos in DUP in order to support bcftools conversion.
2. Correct REF and ALT fields. Adjust END value of INS to make it equal to the value of POS.
3. Improve the description of errors.
4. Add usegalaxy.eu badge.
5. Remove CHR2 and the corresponding END position on the BND call.
6. Skip generating empty signature file and rewrite the job schedule.
7. Add force calling function and enable cuteSV to perform population-based SV calling.
8. Fix several minor bugs.

1. Rewirte the function of ins/del signatures clustering.
2. Update the recommandation parameters for different sequencing datasets.
3. Replace \<DEL\>/\<INS\> with its variant allele sequence, which needs the reference genome sequence as input.
4. Fix several bugs.