added fix to skip segments with no mapped reads

cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.

GNU Affero General Public License v3.0

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added fix to skip segments with no mapped reads #79

Closed sb43 closed 5 years ago

sb43 commented 5 years ago

This resolves bug # 65 : get_rg_cns.R fails when sample does not have any reads in the segment bug

sb43 commented 5 years ago

@keiranmraine please check all the changes before I merge the branch. Results are identical with the brass version 6.1.2 in canpipe live for samples in test project 1404.

sb43 commented 5 years ago

Comparison with gold project 4764 has no differences when compared "*.annot.bedpe" files