Add soapsnp calibration test data for angsd/dosaf module - #2183
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Description
Adds an additional test dataset required for the
angsd/dosafmodule (site allele frequency likelihood estimation).This dataset consists of soapSNP calibration files produced by the upstream
angsd/soapsnpcalibrationprocess, needed to testangsd/dosafwhen run with-GL 3(soapSNP genotype likelihood model), which requires a calibration directory to be passed via-tmpdir.The calibration directory contains two file types per test sample:
*.counts*: per-position base/allele counts*.qual*: recalibrated quality score informationThe calibration directory has been added to data/delete_me/angsd as I cannot identify a more suitable location. If there is please let me know.
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