robegan21
commented
9 years ago I'm glad to hear that you've integrated ALE, and sorry that you've come across an issue.
That error means there is an invalid record in your BAM or SAM file, where the CIGAR string indicates a differently sized sequence than is present in the sequence field. ALE requires the BAM files to be fully compliant and performs checks to ensure the data is valid. How was this alignment file generated -- with what tool?
You can either: 1) remove the offending alignment record, which arguably might be hard to track down without a debugger and experience in C. 2) re-compile with -DNDEBUG flag to disable this assertion (with unknown side effects) 3) remove or comment out line 618 in src/ALElike.c and recompile (again with unknown side effects) 4) share your BAM and reference with me and I can help track down the data issue.
-Rob
I have integrated ALE in a pipeline I run on a large number of samples. For some reason I get the error: _ALE: ALElike.c:618: getContributionsForPositions: Assertion `seqPos == read->core.lqseq' failed. But only for a few assemblies of a few samples. As I am not a C programmer I don't really understand what is going wrong here...