Release pangene-1.1 (r231)

lh3 · Feb 22, 2024 · c9e00aa · c9e00aa
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diff --git a/NEWS.md 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
@@ -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
@@ -3,7 +3,7 @@
 
 #include <stdint.h>
 
-#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
@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-const pg_version = "r220-dirty";
+const pg_version = "1.1-r231";
 
 /**************
  * From k8.js *