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TheJacksonLaboratory / diachromatic

Diachromatic is a Java application for preprocessing and quality control of Hi-C and CHi-C data.
https://diachromatic.readthedocs.io/en/latest/
GNU General Public License v3.0
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NullPointerException for align step with hg38 #135

Closed hansenp closed 5 years ago

hansenp commented 5 years ago

The digest map generated by GOPHER does not contain the chrEBV. If the index for bowtie2 contains chrEBV this causes a NullPointerException for read pairs mapped to this chromosome.

hansenp commented 5 years ago

We could throw and catch an exception ChromosomeNotInDigestMap.