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docs: Add remote bam support and fix aux-tag argument name #2

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Merged
fxwiegand merged 3 commits into from
Oct 7, 2026
Merged

docs: Add remote bam support and fix aux-tag argument name #2

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docs: Add remote bam support and fix aux-tag argument name
fxwiegand Oct 7, 2026
c120d24
docs: Make highlight name optional
fxwiegand Oct 7, 2026
6c3c260
Merge remote-tracking branch 'origin/main' into docs/update-arguments
fxwiegand Oct 7, 2026
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2 changes: 1 addition & 1 deletion src/config.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
project:
name: Alignoth
version: 1.10.0
version: 1.11.1
copyright: 2024, Koesterlab
authors: Felix Wiegand, Johannes Koester

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6 changes: 3 additions & 3 deletions src/docs/usage.rst
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Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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.
-
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