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Fix 4dExtract problem w/ intra-exon duplication

(hopefully)
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1 parent 01df73c commit bba26fefd6accc141b8f8cc153887fba8650ab6f @joelarmstrong joelarmstrong committed Nov 15, 2013
Showing with 4 additions and 2 deletions.
  1. +4 −2 extract/impl/hal4dExtract.cpp
@@ -264,9 +264,11 @@ void Extract4d::extractConservedBlocks4d()
if (reversed) {
colIt->toSite(colIt->getReferenceSequencePosition() + _refSequence->getStartPosition() - 1,
colIt->getReferenceSequencePosition() + _refSequence->getStartPosition(),
- false);
+ true);
} else {
- colIt->toRight();
+ colIt->toSite(colIt->getReferenceSequencePosition() + _refSequence->getStartPosition() + 1,
+ colIt->getReferenceSequencePosition() + _refSequence->getStartPosition() + 2,
+ true);
}
}
}

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