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Re: [Seqan-dev] Asymmetric Scoring of Insertions / Deletions in Alignments

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Thanks Rene,

That appears to let me create the type of scoring schemes I need, but it looks like "computeAlignmentStats" function can't quite handle the polymorphism yet:

"""
In file included from /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/pbsparse/src/ControlFilter.cpp:50:
In file included from /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/pbsparse/include/pbsparse/FindSeedsConfig.h:40:
In file included from /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/align.h:55:
In file included from /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/graph_align.h:45:
In file included from /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/score.h:49:
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/score/score_simple.h:224:15: error: no member
      named 'data_gap_open' in 'seqan::Score<long, const seqan::Tag<seqan::BiAffine_> >'
    return me.data_gap_open;
           ~~ ^
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/align/evaluate_alignment.h:227:41: note: in
      instantiation of function template specialization 'seqan::scoreGapOpen<long, const seqan::Tag<seqan::BiAffine_> >' requested here
                stats.alignmentScore += scoreGapOpen(scoringScheme);
                                        ^
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/pbsparse/include/pbsparse/BandedAligner.h:300:9: note: in instantiation of function template
      specialization 'seqan::computeAlignmentStats<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<void> >, seqan::Tag<seqan::ArrayGaps_>, long, const
      seqan::Tag<seqan::BiAffine_> >' requested here
        computeAlignmentStats(stats, align, scoringScheme_);
"""

-B

On Wed, Jun 3, 2015 at 8:21 AM, Rahn, René <rene.maerker@fu-berlin.de> wrote:
Hi Brett, 

this is possible with the BiAffine Score specification.
However this was so far only used in the JournaledStringSet module which is still under development.
You can access it by simply including <seqan/journaled_set/score_biaffine.h>

You can use the setter and getter functions:

setScore/score
setScoreMismatch/scoreMismatch
setScoreGapOpenVertical/scoreGapOpenVertical
setScoreGapOpenHorizontal/scoreGapOpenHorizontal
and of course the standard setGap interfaces.

Apart from this, the entire align engine for the standard DP algorithms works with different gap penalties for insertions/deletions.

Cheers,

René



On 26 May 2015, at 23:57, Brett Bowman <bnbowman@gmail.com> wrote:

I'd like to create some scoring schemes with asymmetric weights for insertion / deletion errors for working with single-molecule sequencing data.  Raw data from both PacBio and Oxford Nanopore have known insertion-biases, and so optimal scoring schemes need to penalize those errors less than deletions. 

This appears to be partially supported by the SeqAn API already, since the "Score" class has separate interface functions for "scoreGapHorizontal" and "scoreGapVertical", but I can't see any existing specifications that utilize them.

Is there an allowed / recommended way to do this currently, or do I need to create my own Score specialization?

Sincerely,
-Brett
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---

René Rahn
Ph.D. Student
--------------------------------
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Institute of Computer Science
Algorithmic Bioinformatics (ABI)
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Freie Universität Berlin
Takustraße 9
14195 Berlin
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