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berman-lab / ymap

YMAP - Yeast Mapping Analysis Pipeline : An online pipeline for the analysis of yeast genomic datasets.
MIT License
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Chromosomes that don't have any reads mapping to them can crash the analysis #39

Closed vladimirg closed 7 years ago

vladimirg commented 8 years ago

In processing1.m (which calls CNV_v6_6.m), if the chr_CNVdata contains zeros for the entire chromosome, it may later crash in CNV_v6_6.m:437 because fitY2 (and other Y-related variables) will have bad values (NaN, inf).

We should instead mark these regions (for the user as well, to make them aware of the issue) and ignore them in downstream analysis, to prevent the crash.