From 41941ff29fbd62bcfddabc9471f520f99ad71a6d Mon Sep 17 00:00:00 2001 From: fxwiegand Date: Wed, 7 Oct 2026 11:08:47 +0200 Subject: [PATCH 1/2] docs: Add remote bam support and fix aux-tag argument name --- src/config.yaml | 2 +- src/docs/usage.rst | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/config.yaml b/src/config.yaml index 0fc7171..53575e2 100644 --- a/src/config.yaml +++ b/src/config.yaml @@ -1,6 +1,6 @@ project: name: Alignoth - version: 1.10.0 + version: 1.11.1 copyright: 2024, Koesterlab authors: Felix Wiegand, Johannes Koester diff --git a/src/docs/usage.rst b/src/docs/usage.rst index f11b67f..7b16cb4 100644 --- a/src/docs/usage.rst +++ b/src/docs/usage.rst @@ -39,7 +39,7 @@ Arguments - default * - bam-path - -b - - BAM file(s) to be visualized. Multiple files can be given (e.g. ``-b a.bam -b b.bam``) and will be stacked in the resulting plot. + - BAM file(s) to be visualized. Accepts local paths or ``http(s)``/``ftp`` URLs like samtools. Remote files need a matching index (``.bai``/``.csi``). Multiple files can be given (e.g. ``-b a.bam -b b.bam``) and will be stacked in the resulting plot. - * - reference - -r @@ -85,7 +85,7 @@ Arguments - -f - Sets the output format for the read, reference and highlight data - json - * - aux_tag + * - aux-tag - -x - Displays the given content of the aux tag in the tooltip of the plot. Multiple usage for more than one tag is possible. - From c120d243c92124c209f20989700964b1951f400f Mon Sep 17 00:00:00 2001 From: fxwiegand Date: Wed, 7 Oct 2026 11:17:03 +0200 Subject: [PATCH 2/2] docs: Make highlight name optional --- src/docs/usage.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/docs/usage.rst b/src/docs/usage.rst index 7b16cb4..0d854d6 100644 --- a/src/docs/usage.rst +++ b/src/docs/usage.rst @@ -55,7 +55,7 @@ Arguments - * - highlight - -h - - Named intervals or single base positions that will be highlighted in the visualization. Example: myinterval:132400-132500 or myvariant:132440 + - Interval or single base position that will be highlighted in the visualization, optionally prefixed with a name. Example: 132440-132450, 132440, myinterval:132440-132450 or myvariant:132440 - * - vcf - -v