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duncanca / mosaik-aligner

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Error in SAM column ISIZE on a negative ISIZE value (Bug in MosaikText.cpp:720). #94

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
MosaikText -in example.dat -sam example.sam

What is the expected output? What do you see instead?
Negative ISIZE value as in MosaikText made BAM file.

What version of the product are you using? On what operating system?
MosaikText 1.1.0021

Please provide any additional information below.

Row 720 in MosaikText.cpp contains:
gzprintf(mStreams.sam, "=\t%u\t%u\t", alIter->MateReferenceBegin + 1, 
insertSize);

However, insertSize is in fact a int which could some times be negative. This 
line should use %d or %i, not %u (unsigned):

gzprintf(mStreams.sam, "=\t%u\t%d\t", alIter->MateReferenceBegin + 1, 
insertSize);

Original issue reported on code.google.com by dr.isaks...@gmail.com on 1 Mar 2011 at 5:28