[Seqan-dev] Cannonical Alignment Row Ordering
- From: Brett Bowman <bnbowman@gmail.com>
- To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Date: Fri, 5 Jun 2015 11:47:38 -0700
- Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Subject: [Seqan-dev] Cannonical Alignment Row Ordering
Is there a standardized way to order sequences in Alignment objects in SeqAn?
Reason being that the code in "align/evalulate_alignment.h" appears to take Row #0 as the reference:
"""
// Get iterators.
TGapsIter it0 = begin(row(align, 0));
TGapsIter itEnd0 = end(row(align, 0));
TGapsIter it1 = begin(row(align, 1));
TGapsIter itEnd1 = end(row(align, 1));
for (; it0 != itEnd0 && it1 != itEnd1; ++it0, ++it1)
{
if (isGap(it0))
{
stats.numDeletions += 1;
}
if (isGap(it1))
{
stats.numInsertions += 1;
}
}
"""
While the code for writing alignments in "align/align_base.h" prints rows in numerical order, which puts the query below the reference, in an inversion of standard practice:
"""
Reference ATCTCTCTC-A-ACAACAA--CAACGGAGGAGG-AGGAAAAGAGAGAGAT
Align |||||||||*|*|||||||**||||||||||||*||||||||||||||||
Query ATCTCTCTCAACACAACAACGCAACGGAGGAGGAAGGAAAAGAGAGAGAT
"""
"""
assignSource(row(alignment, 0), sequenceH);
assignSource(row(alignment, 1), sequenceV);
Score<int, Simple> scoringScheme(2, -1, -2);
int result = bandedChainAlignment(alignment, seedChain, scoringScheme, 2);
"""
assignSource(row(alignment, 1), sequenceV);
Score<int, Simple> scoringScheme(2, -1, -2);
int result = bandedChainAlignment(alignment, seedChain, scoringScheme, 2);
"""
-Brett
-
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