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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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Infinite loop if file does not exist #31

Open dsenalik opened 8 years ago

dsenalik commented 8 years ago

In file src/bddata.cpp line 42 (and elsewhere) a file is opened, but is not checked for existence beforehand, nor checked after open, e.g. CheckbdFileFirst.good() If the file does not exist, an infinite loop condition occurs because CheckbdFileFirst.eof() is never true.

EWLameijer commented 8 years ago

Thank you again! Basically same reply here, solving some khash-problems has my current priority, but this is definitely an area where Pindel could have been programmed more cleany. So thank you for providing some extra eyes to the code!