v3.0.3

Major change

Introduce the -salvage [0|1] flag (default: 0) to recycle intermediate files and skip reruns when -salvage 1 is specified. This is particularly useful when processing large genomes (> 10 Gb) with limited walltime.

• Reuse existing results in the Init, Major, and Trunc steps to skip reprocessing.
• In the Major step, reuse TEsorter, HMM classification files, and processed candidates in the .defalse file.
• Add new utility scripts under bin/:
  - bed_intersect_wao.pl: bedtools-like intersect with ‘wao’ behavior and buffer
  - filter_extend.fa_by_defalse.pl: filters extended FASTA by existing entries in the .defalse file
  - filter_scn_by_defalse.pl: filters scn entries present in .defalse file

Minor change

Modify LTR.identifier.pl:
- Make necessary changes to implement the salvage mode.
- Add fallback for zero-length boundaries ($tot_len = $seq_len) to fix @EDTA#564

Full Changelog: v3.0.2...v3.0.3