Biostar139647 : documentation issues

[blinard-BIOINFO]

Subject of the issue

Biostar139647 : documentation issues

• Documentation should comment that the format conversion does not allow to select a reference from inside the clustal alignment
• Documentation should comment that Insertions are not handled, only matches and Deletions
• Documentation should comment that heading and trailing gaps are NOT consider as real indels (compared to a virtual reference genome) but start/ends of mapped reads

Steps to reproduce

If one of the alignment sequence is considered as the reference genome, then the output sam is incorrect (because no alignment sequence can be selected as reference)? In particular, insertions to the reference are not handled.

Expected behaviour

This is fine, but should be clarified in the documentation.

[lindenb]

Thanks feel , that was a tool made quickly for biostars.org , but fell free to submit a PR to insert all those informations.

[blinard-BIOINFO]

Answer in PR #228