Release 0.9.0
Fixed
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Fixed issue that peptides caused by start gain mutations are not called by
bruteForce
. #492 -
Fixed issue that variant peptides caused by start gain mutations from noncoding transcripts are not called in some cases. Stop gain mutations from downstream are also missed in some cases. #495
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Fixed issue that some variant peptides were not called with in-frame deletions. #515
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Fixed issue that the shuffled decoy sequences produced by decoyFasta are not reproducible when input FASTA order is changed. #517
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Fixed issue that stop lost mutations are not recognized correctly. #519
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Fixed issue that start gain and stop lost mutations before the novel start site were not excluded. #520
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Fixed issue that frameshifting mutations on the same node of a novel ORF start site and is right after it was not carried over to downstream nodes. #526
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Fixed issue that stop lost mutations were not recognized for deletions. #527
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Fixed issue that in-frame deletion stop retaining mutations were not recognized #528
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Fixed issue that variant coordinates not handled correctly when the cleavage site is contained in the inserted sequence. #52
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Fixed issue that peptides are not called with overlapping deletions. #531