Feature: Align and Extend

[Adamtaranto]

Existing modules:

• Base Teloclip extracts any reads that are soft-clipped at contig ends (optionally checking for telomeric motifs)
• Teloclip-extract: bins reads from teloclip into output files per contig end (left / right for each contig)

New module:

• Teloclip-extend: Extend a contig with the soft-clipped overhang of a single aligned read or contig.

Tasks:

• Write function that takes a single aligned read and extends a contig with the overhanging (soft-clipped) segment of the alignment.
• Handle cases where alignment is clipped at both ends of contig
• Update argparser to use submodule keywords [filter, extract, extend]

[Adamtaranto]

Proposed modules names:

teloclip filter
teloclip extract
teloclip extend

[Adamtaranto]

#10 requests automation of the contig extension process. I think it is generally unwise to blindly accept overhang alignments are "real" without inspecting them first.

Need to balance convenience vs enabling errors.

Could provide tutorial on manual curation: Select the best overhang-read (i.e. confident anchor region, unique alignment, many reads agree) and then extend contig with teloclip extend.

Alternatively, could provide an extend-now-ask-questions-later option whereby we extend contigs using the longest available overhang and then suggest validation checks i.e. align all overhang-reads back to the extended contig and look for agreement between reads.

[Adamtaranto]

Add output option for extract to yield MAF or MSA of overhang-reads that can be viewed in terminal or externally.

[Adamtaranto]

Note: Log total bases extended and bases per contig end. Useful for reporting results.

[Adamtaranto]

Option: Output BED file coords for extended sequence segments for review.