OBIKmers/obikmer
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Push zpwxxpnpktps #67

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coissac merged 46 commits from push-zpwxxpnpktps into main 2026-08-17 09:41:42 +00:00
Conversation 0 Commits 46 Files Changed 405
+7 -5
3 changed files with 7 additions and 5 deletions
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src/Cargo.lock
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+1 -1
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@@ -1793,7 +1793,7 @@ dependencies = [
[[package]] [[package]]
name = "obikmer" name = "obikmer"
version = "1.1.44" version = "1.2.0"
dependencies = [ dependencies = [
"clap", "clap",
"csv", "csv",
src/obikmer/Cargo.toml
+1 -1
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@@ -1,6 +1,6 @@
[package] [package]
name = "obikmer" name = "obikmer"
version = "1.1.44" version = "1.2.0"
edition = "2024" edition = "2024"
[[bin]] [[bin]]
src/obikmer/src/cmd/phylo/tnt.rs
+5 -3
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@@ -46,6 +46,10 @@ pub(super) fn write_sankoff_tnt(
let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0); let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
writeln!(f, "xread").unwrap(); writeln!(f, "xread").unwrap();
writeln!(f, "mxram 16000;").unwrap();
writeln!(f, "taxname =;").unwrap();
writeln!(f, "taxname +50;").unwrap();
writeln!( writeln!(
f, f,
"'obikmer central-position SNP families, calibrated Sankoff 16-state encoding'" "'obikmer central-position SNP families, calibrated Sankoff 16-state encoding'"
@@ -166,9 +170,7 @@ pub(super) fn write_sankoff_tnt(
writeln!(f, ";").unwrap(); writeln!(f, ";").unwrap();
writeln!(f, "hold 20;").unwrap(); writeln!(f, "hold 20;").unwrap();
writeln!(f, "mult;").unwrap(); writeln!(f, "mult;").unwrap();
writeln!(f, "taxname =;").unwrap(); writeln!(f, "export - {tre_name};").unwrap();
writeln!(f, "tsave * {tre_name};").unwrap();
writeln!(f, "tsave /;").unwrap();
info!( info!(
"TNT script → {path} (costs scaled x{cost_scale:.0}, runs a default `hold 20; mult;` \ "TNT script → {path} (costs scaled x{cost_scale:.0}, runs a default `hold 20; mult;` \