local search (-ls) bug - Githubissues

GoogleCodeExporter commented 8 years ago

many uniquely mapped pairs found without -ls are reported as both pairs
non-unique when -ls local search is enabled.  Upon inspection the
additional "non-unique" mappings are to nonsense locations in the genome
(i.e. coordinates that do not exist).  Is suspect that there's a bug in the
refIndex and the begin/end coordinate handling in the local-search code
that is making the same (re-discovered) mate pair alignments erroneously
look novel (such that alignment.Add() isn't catching them).  Easier to
explain by phone than by email/text: 434-982-6583 --Aaron Mackey

Original issue reported on code.google.com by ajmac...@gmail.com on 10 Nov 2009 at 2:13

GoogleCodeExporter commented 8 years ago

looks like there are already some SVN commits related to this issue ... I'll 
retest
with today's SVN checkout

Original comment by ajmac...@gmail.com on 10 Nov 2009 at 2:53

GoogleCodeExporter commented 8 years ago

I encountered the same issue with local search (-ls).

Xiaoping

Original comment by xiaoping...@stjude.org on 10 Nov 2009 at 3:06

GoogleCodeExporter commented 8 years ago

FYI, this seems to be fixed

Original comment by ajmac...@gmail.com on 9 Dec 2009 at 4:29

GoogleCodeExporter commented 8 years ago

Thanks for checking this Aaron. 

I was about to suggest trying the new version that we just released this week 
(1370)
to see if that also resolves your problem.

Cheers,

// Michael

Original comment by snowneb...@gmail.com on 16 Jan 2010 at 2:06

Changed state: Fixed

guanchangge / mosaik-aligner

local search (-ls) bug #16