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Fixed wrong order of parameters for the LAmerge call. #7

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@isovic isovic commented Jul 10, 2017

Datander crashed due to the wrong paths.

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isovic commented Jul 10, 2017

The second commit is a fix for empty overlap files which might be generated in some cases.

I attempted to run DAMASKER on a small example (attached) but received this error:
TANmask: .las file overlaps don't correspond to reads in block 9 of DB.

Upon inspection, it seems that the blocks db.T.[3,6,9,16,18].las were empty (except for 12B used to store novl (8B) and TRACE_SPACING (4B)).
I noticed that there is no check for the number of overlaps in the input file before accessing the first entry.
This pull request adds just a simple check, and returns 0 (the value which would be returned if the for loop is never executed).

A self-contained example is attached here:
bug-example.tar.gz

The dataset in this example is a subset of PacBio reads which align to K-12 reference in between [300000-400000>bp.

Please note that, without incorporating the first fix in this pull request, the example will fail on LAmerge.

Thank you,
Best regards,
Ivan.

CC: @pb-cdunn

pacbbbbot pushed a commit to PacificBiosciences/DAMASKER that referenced this pull request Apr 4, 2018
…47-DISCLAIMER to develop

* commit '637c70d2420733373c08c53979bb8fe0fe7bd949':
  Added DISCLAIMER
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