From a8c9987947127a8080d8a8cc24738631d75064af Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Wed, 15 Jun 2011 10:06:17 +0200
Subject: [PATCH] Fiex bug with sequence offsets
---
modules/seq/alg/src/merge_pairwise_alignments.cc | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/modules/seq/alg/src/merge_pairwise_alignments.cc b/modules/seq/alg/src/merge_pairwise_alignments.cc
index 6bba7edd0..032e92ac9 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.cc
+++ b/modules/seq/alg/src/merge_pairwise_alignments.cc
@@ -55,7 +55,8 @@ void update_shifts(const AlignmentHandle& aln,
res_index=-1;
}
else if (i > 0) {
- res_index=s1.GetResidueIndex(i-1);
+ res_index=s1.GetResidueIndex(i-1)-s1.GetOffset();
+// res_index=s1.GetResidueIndex(i-1);
}
ShiftMap::iterator p=shifts.find(res_index);
if (p!=shifts.end()) {
@@ -111,7 +112,8 @@ SequenceHandle realign_sequence(const AlignmentHandle& aln,
p=shifts.find(-1);
}
else if (i>0 && s1.GetOneLetterCode(i-1)!='-') {
- p=shifts.find(s1.GetResidueIndex(i-1));
+ p=shifts.find(s1.GetResidueIndex(i-1)-s1.GetOffset());
+// p=shifts.find(s1.GetResidueIndex(i-1));
}
if (p!=shifts.end()) {
int d=p->second-shift;
@@ -139,6 +141,7 @@ AlignmentHandle MergePairwiseAlignments(const AlignmentList& pairwise_alns,
update_shifts(*i, ref_seq, shifts);
}
+
AlignmentHandle merged=CreateAlignment();
merged.AddSequence(shift_reference(ref_seq, shifts));
for (AlignmentList::const_iterator i=pairwise_alns.begin(),
--
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