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genome / pindel

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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-j option easily leads to segfault

mwyczalkowski opened this issue · comments

commented

A misformed BED file passed as an argument to the -j argument leads to segmentation faults, which can be hard to diagnose.

  • Specifying a chrom in the BED which is not in reference will lead to seg fault
  • Having a comment ("# comment") in BED file will lead to seg fault (such comments are allowed in BED file specifications)

In general, implementing basic error checking when parsing this file and reporting errors more explicitly would be very helpful to the user.