c-zhou/yahs: YaHS-1.2

Major changes in this release.

1. Improved compatibility with AGP specifications. The default component type is now 'U' (previously 'N'). The default gap size is now 100 (previously 200). The default linkage evidence is now 'proximity_ligation' ( previously 'na'). These defaults can be adjusted using parameters '--gap-ctype', '--gap-size' and '--gap-link', respectively. For more details, refer to the full help message by running yahs -?.

2. The scaffolding logic has been updated. In previous versions, the scaffolding process would stop if the N50 was too small for a given resolution. Now, the process will attempt additional rounds of scaffolding at the previous resolution level and will only terminate if there are still no significant improvements.

3. A new '-R' option has been added to control the number of rounds to run at each resolution level.

4. A telomeric sequence identification module has been integrated to detect chromosome ends. Sequences identified as telomeric will be prevented from joining other sequences. YaHS includes a default telomeric motif database (you can view the list by running yahs --print-telo-motifs). The --telo-motif option can be used to specify a custom telomeric motif. When this option is set, only the specified motif will be checked. The code for telomere identification was adopted from seqtk telo.