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CHANGES.txt
42 lines (36 loc) · 1.9 KB
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CHANGES.txt
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v0.3.5a
---
* JCAST will now skip a junction if the nucleotide sequence contains masked bases
* Added the --mask argument to determine masked nucleotide letters (default: NnXx)
* Added an option to translate only a subset of splice types (MXE, RI, SE, A3SS, A5SS) with the -s argument
v0.3.5
---
* Fixed issue where a small number of slices were not translated.
v0.3.3
---
* Fixed bug when model flag is not set
v0.3.2
---
* The -q --qvalue option now works by including splice junctions within the specified range. To
preserve the previous behavior, use -q 0.01 1. The default -q 0 1 disables filtering.
* The -c --canonical argument now defaults to False. To preserve prior behaviors, manually set the
-c flag to translate canonical proteins detected in the RNA-seq experiments even if isoform translation failes
* The -c --canonical argument now will translate a canonical sequence even if a splice event has low skipped
junction counts or falls outside of the specified fdr range
* JCAST now automatically models the likely translatable junction count threshold through the -m --model argument.
Previously this was done manually then set as an integer (minimal read count) using the -r --read argument.
* The skipped junction counts used for modeling now consider the sum of all biological and technical replicates
rather than the minimum
v0.3.1
---
* Fixed issues where Gencode GTF files without transcript_biotype annotations could not be read
* Fixed issues of retrieving Uniprot canonical sequences from Ensembl transcript versions
* Compatibility with biopython>=1.78
v0.2.8
---
* Fixed an issue where jcast is called twice from the direct cli entry point
* Added option to use longest coding sequence from GTF as canonical
v0.2.6
---
* Fixed an issue where some A5SS minus-strand transcripts had incorrect phases retrieved from gtf
* Fixed an issue where some transcripts using a secondary translation start sites are not trimmed