Use breakpoint homology to refine junction spanning read counts

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Thanks to the deFuse project for this nice idea.

For each candidate chimera, compare the sequence of the candidate 3' partner 
with the sequence of the normal gene.  Count the number of bases of exact 
homology at the junction and include this information when remapping to find 
junction spanning reads.

When tallying the junction spanning reads, only count reads that span further 
than the regions of homology in the 5'/3' partners.

Implementing this additional filter is trivial and should account for a lot of 
the candidates with large numbers of junction-spanning reads with a small 
amount of "anchor".

Not high priority because we have other means of filtering these reads.

Original issue reported on code.google.com by matthew....@gmail.com on 5 Feb 2011 at 4:57

[GoogleCodeExporter]

Added this -- was trivial

Original comment by matthew....@gmail.com on 6 Feb 2011 at 5:05

• Changed state: Fixed