Bug Fixes
- Fixed a "file not found" error when calling the hlapers executable in the PATH
Changes
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Instead of personalizing the references for all HLA loci included in the IMGT repository, now personalizations is applied to the following loci only: A, B, C, E, F, G, H, DMA, DMB, DOA, DOB, DPA1, DPA2, DPB1, DPB2, DQA1, DQA2, DQB1, DRA, DRB1, DRB3, DRB4, DRB5.
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There is a new method for quantification: Salmon-reads, which uses the Salmon lightweight alignment algorithm.
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New option to sort BAM files by coordinates, which is necessary when extracting reads from the MHC region for genotyping.