Handling of unknown intron positions (e.g. x.a-?_b+?del)
Created by: mutalyzerbot
Original ticket: https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/38 Original date: 2011/02/28 Original reporter: m DOT vermaat DOT hg AND lumc DOT nl
Current solution is to substitute 0 for the question marks.
Proposed solution: Interpret ? as the middle position of the intron, but never explicitely show this number in c. notation.
Example: a b
====-------------===========-------------========
\___________/ \___________/
2000b 5000b
Original description: c.a-?_b+?del
Internally handle this as: c.(a-1000_b+2500)del
From this, calculate: g.(34299_23232)del
Never show the c.(a-1000_b+2500)del to the user. The brackets ( and ) denote that the exact positions are uncertain.