fix bug in halAlignability and halPhyloPMain where more than the tota…

…l length could be computed due to a bug in chopping into sequence coordinates
ComparativeGenomicsToolkit · Jul 26, 2013 · 0b26b99 · 0b26b99
1 parent b825fbf
commit 0b26b99
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/alignability/halAlignability.cpp b/alignability/halAlignability.cpp
@@ -388,7 +388,7 @@ void printGenome(ostream& outStream,
       {
         hal_size_t readStart = seqStart >= start ? 0 : start - seqStart;
         hal_size_t readLen = min(seqLen - readStart, length);
-
+        readLen = min(readLen, length - runningLength);
         printSequence(outStream, sequence, targetSet, readStart, readLen, step);
         runningLength += readLen;
       }

diff --git a/phyloP/impl/halPhyloPMain.cpp b/phyloP/impl/halPhyloPMain.cpp
@@ -248,7 +248,7 @@ void printGenome(PhyloP *phyloP,
       {
         hal_size_t readStart = seqStart >= start ? 0 : start - seqStart;
         hal_size_t readLen = min(seqLen - readStart, length);
-
+        readLen = min(readLen, length - runningLength);
         phyloP->processSequence(sequence, readStart, readLen, step);
         runningLength += readLen;
       }