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apeltzer / CircularMapper

A method to improve mappings on circular genomes, using the BWA mapper
GNU General Public License v3.0
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String index out of range #5

Open JudithNeukamm opened 7 years ago

JudithNeukamm commented 7 years ago

Class "ReadTrimmer" (line 114) throws a StringIndexOutOfBoundsException, if variable "pos" is equal the length of the sequence.

jonaudet commented 6 years ago

Having a similar issue (but at line 119).

apeltzer commented 6 years ago

I unfortunately think this is a bug - will try updating the library and have a look at this. Do you have some test samples for these?

JudithNeukamm commented 5 years ago

For me, it happens when mapping this sample (SRR5832640) against M.leprae. I can also send you the xml file if required.

apeltzer commented 5 years ago

nice thank you! I'll download the sample and set up test cases for fixing this then :-)