From 6c4a6c697c6f460acff64c2e6de5f7b8733f6871 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Thu, 30 Apr 2026 16:57:45 +0200 Subject: [PATCH] [4.4.2] Enhanced taxonomy handling, input robustness & PCR tag validation - **obiconvert**: Added `--raw-taxid` mode to output numeric taxIDs without formatting (e.g., "12345" instead of ":tax:NCBI_0987@species"). Introduced `TaxNode.FullString()` to reliably return full formatted strings regardless of global settings, and improved fallback behavior when taxonomy DB is unavailable. - **ngsfilter**: Input fields (primers, sample tags/IDs) are now automatically trimmed of leading/trailing whitespace to prevent parsing failures from inconsistent formatting. - **obitools (pcrtag)**: Mismatch-related fields (`forward_mismatches`, `reverse_mishaps`) renamed to "error" for consistency across annotation dictionaries. - **obipairing & obtagpcr**: Enforced mandatory paired-end file input (`--forward` and `reverse`) in obipairing; added CLI support for generating config templates via AskConfigTemplate(); removed redundant `Required()` constraints and introduced helper function CLIHasPairedFiles(). --- pkg/obioptions/version.go | 2 +- version.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go index 3a47141..ef7733c 100644 --- a/pkg/obioptions/version.go +++ b/pkg/obioptions/version.go @@ -3,7 +3,7 @@ package obioptions // Version is automatically updated by the Makefile from version.txt // The patch number (third digit) is incremented on each push to the repository -var _Version = "Release 4.4.41" +var _Version = "Release 4.4.42" // Version returns the version of the obitools package. // diff --git a/version.txt b/version.txt index 8be79b9..cdc0aa1 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -4.4.41 +4.4.42