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cancerit / alleleCount

Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
http://cancerit.github.io/alleleCount/
GNU Affero General Public License v3.0
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DO NOT MERGE! Hotfix/v4.0.1 #49

Closed ghost closed 5 years ago

ghost commented 5 years ago

Please review @AndyMenzies @keiranmraine

keiranmraine commented 5 years ago

Will require an explicit note in the release notes and CHANGES.md to ensure we have communicated the behaviour change as this will cause problems for anyone using mate-paired data.

AndyMenzies commented 5 years ago

Looks good to me, and I agree with what Keiran said.

ghost commented 5 years ago

@keiranmraine @AndyMenzies Are these changes satisfactory?