docs: add issues #86 and #87 to release notes

ktmeaton · Oct 3, 2022 · d56956d · d56956d
1 parent 00a706a
commit d56956d
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/docs/notes/Notes_v0.4.3.md b/docs/notes/Notes_v0.4.3.md
@@ -22,8 +22,10 @@ This is a minor bug fix and enhancement release with the following changes:
 - [Issue #79](https://github.com/ktmeaton/ncov-recombinant/issues/79): Add new parameter `min_consec_allele` to `sc2rf_recombinants` to ignore recombinant regions with less than this number of consecutive alleles (both diagnostic SNPs and diganostic reference alleles).
 - [Issue #80](https://github.com/ktmeaton/ncov-recombinant/issues/80): Migrate [sc2rf](https://github.com/lenaschimmel/sc2rf) froma submodule to a subdirectory (including LICENSE!). This is to simplify the updating process and avoid errors where submodules became out of sync with the main pipeline.
 - [Issue #83](https://github.com/ktmeaton/ncov-recombinant/issues/83): Improve error handling in `sc2rf_recombinants` when the input stats files are empty.
-- [Issue #89](https://github.com/ktmeaton/ncov-recombinant/issues/89): Reduce the default value of the parmaeter `min_len` in `sc2rf_recombinants` from 1000 to 800.This is to handle `XAP`, which has a `BA.1` recombinant regions of `854` nucleotides.
-- [Issue #90](https://github.com/ktmeaton/ncov-recombinant/issues/90): Auto-pass select nextclade lineages through sc2rf: `XN`, `XP`, `XAS`, and `XAZ`. This requires differentiating the nextclade inputs as separate parameters `--nextclade` and `--nextclade-no-recom`.
+- [Issue #86](https://github.com/ktmeaton/ncov-recombinant/issues/87): Auto-pass `XAS` through `sc2rf`.
+- [Issue #87](https://github.com/ktmeaton/ncov-recombinant/issues/87): Auto-pass `XAZ` through `sc2rf`.
+- [Issue #89](https://github.com/ktmeaton/ncov-recombinant/issues/89): Reduce the default value of the parmaeter `min_len` in `sc2rf_recombinants` from `1000` to `800`.This is to handle `XAP`, which has a `BA.1` recombinant regions of `854` nucleotides.
+- [Issue #90](https://github.com/ktmeaton/ncov-recombinant/issues/90): Auto-pass select nextclade lineages through `sc2rf`: `XN`, `XP`, `XAS`, and `XAZ`. This requires differentiating the nextclade inputs as separate parameters `--nextclade` and `--nextclade-no-recom`.
 
     `XN` and `XP` have extremely small recombinant regions at the terminal ends of the genome. Depending on sequencing coverage, `sc2rf` may not reliably detect these lineages.