From c9e00aab16fae776e73fcbe2761c645ef98747c4 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 22 Feb 2024 11:16:33 -0500 Subject: [PATCH] Release pangene-1.1 (r231) --- NEWS.md | 23 +++++++++++++++++++++++ pangene.1 | 2 +- pangene.h | 2 +- pangene.js | 2 +- 4 files changed, 26 insertions(+), 3 deletions(-) create mode 100644 NEWS.md diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..22f1210 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,23 @@ +Release 1.1-r231 (22 February 2024) +----------------------------------- + +Notable changes to pangene: + + * Improvement: more aggressive pseudogene filtering. This helps the great ape + graph. + + * New feature: added option -E to filter out genes aligned with a single exon + in all input genomes. Graphs constructed from multi-exon genes are usually + cleaner. + +Notable changes to pangene.js: + + * Improvement (call): a new bubble finding algorithm via local graph + traversal. Added a filter to remove falsely idenrified bubbles. + + * New feature (call): output names of assemblies that support each allele. + + * New feature: added the getaa subcommand to parse Ensembl and GenCode + annotations. + +(22 February 2024, r231) diff --git a/pangene.1 b/pangene.1 index ad17456..5f5f652 100644 --- a/pangene.1 +++ b/pangene.1 @@ -1,4 +1,4 @@ -.TH pangene 1 "24 October 2023" "pangene-1.0 (r183)" "Bioinformatics tools" +.TH pangene 1 "22 February 2024" "pangene-1.1 (r231)" "Bioinformatics tools" .SH NAME .PP pangene - building pangenome gene graphs diff --git a/pangene.h b/pangene.h index 8b417bf..486ab34 100644 --- a/pangene.h +++ b/pangene.h @@ -3,7 +3,7 @@ #include -#define PG_VERSION "1.0-r223-dirty" +#define PG_VERSION "1.1-r231" #define PG_F_WRITE_BED_RAW 0x1 #define PG_F_WRITE_BED_WALK 0x2 diff --git a/pangene.js b/pangene.js index c9a979b..dfc6812 100755 --- a/pangene.js +++ b/pangene.js @@ -1,6 +1,6 @@ #!/usr/bin/env k8 -const pg_version = "r220-dirty"; +const pg_version = "1.1-r231"; /************** * From k8.js *