diff --git a/README.md b/README.md index 0d7426d..37e4a72 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ Please refer to our [official pbbioconda page](https://github.com/PacificBioscie for information on Installation, Support, License, Copyright, and Disclaimer. ## Latest Version -Version **2.3.0**: [Full changelog here](#full-changelog) +Version **2.4.0**: [Full changelog here](#full-changelog) ## Workflow
@@ -277,8 +277,20 @@ of median length, to have exactly one evidence per molecule. If you don't use it, you will get false positive SV calls and the genotypes will be wrong. +### Why does the VCF contain no ambiguous IUPAC REF codes? +Starting with version 2.4.0, `pbsv` constrains all bases in the reference to be +A,C,T,G,N. Bases unknown (e.g. IUPAC) will be automatically converted to N. +Toggling `--preserve-non-acgt` will retain non A,C,T,G,N bases in the reference. + ## Full Changelog - * **2.3.0**: + * **2.4.0**: + * Ensure identical output for one giant or multiple small svsig files as inputs + * Add `--preserve-non-acgt` + * Fix a problem where signatures in `call` were dropped before target window + * Support non-spanning inversions + * Use incremental VCF ids + + * 2.3.0: * Public release in SMRT Link 9.0.0 * New CLI UX * Change svsig compression to bgzip to enable indexing via tabix