Batch updates

Summarizing updates from v1.1 to v1.3:

Major update

Added the -overlap parameter to allow default 100kb overlap between sequence chunks. This will recover essentially all LTR candidates reported by the original LTR_FINDER. You may still see 1-2 candidates missing due to version changes or random errors. Testing on Arabidopsis, Rice, Maize, and Wheat saw a 0.5% - 5% increase of LTR candidate number from the parallel version likely due to local optimizations of search space. Benchmarking on the Rice genome using LTR_retriever show only marginal changes to the annotation.

Minor updates

1. When -threads 1, LTR_FINDER_parallel will use the default LTR_FINDER without splitting the genome. This could speed up the run on highly fragmented sequences (i.e., raw sequencing reads).
2. Automatically search for and remove DOS newlines in the given sequence file #11
3. improved the parameter for timeout
4. Tested in Cycas_panzhihuaensis.fasta with single sequence as long as 1.2Gb. The stalling on these highly contiguous genomes are resolved.

Full Changelog: v1.1...v1.3