[Biopython-dev] [Biopython - Bug #3234] (New) Bio.HMM Viterbi algorithm: initial state probabilities are wrong

[Phillip Garland]

The patch looks correct to me.

~Phillip

On Mon, May 23, 2011 at 9:03 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Mon, May 23, 2011 at 4:30 PM,  <redmine at redmine.open-bio.org> wrote:
>>
>> Issue #3234 has been reported by Walter Gillett.
>>
>> ----------------------------------------
>> Bug #3234: Bio.HMM Viterbi algorithm: initial state probabilities are wrong
>> https://redmine.open-bio.org/issues/3234
>>
>> Author: Walter Gillett
>> Status: New
>> Priority: Normal
>> Assignee: Walter Gillett
>> Category:
>> Target version:
>> URL:
>>
>>
>> Spun off from #2947, see that bug for discussion. Initial state probabilities
>> should be set explicitly, rather than using the probability of transitioning
>> from a state back to itself, which is incorrect.
>
> Would anyone more familiar with HMMs that I am like to volunteer to review
> Walter's changes? e.g. Philip (CC'd)?
>
> Walter's sent a pull request via github:
> https://github.com/biopython/biopython/pull/6
>
> This consists of two commits, the first an unrelated minor change to the
> ignore file for people using the NetBeans IDE:
> https://github.com/wgillett/biopython/commit/50659de2f0cfa3f0bc913b4ea88d6a001b543d98
>
> Secondly his fix for Bug 3234,
> https://github.com/wgillett/biopython/commit/a60ac226ceed21fd856ff1ec1dbea2782e2172ae
>
> Thanks,
>
> Peter
>