Added _ideogram to tags. More preset ideograms. Updated docs

kcleal · Jul 20, 2024 · f1de08c · f1de08c
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diff --git a/README.rst b/README.rst
@@ -15,7 +15,7 @@ GW
 .. |Dl badge| image:: https://img.shields.io/conda/dn/bioconda/gw.svg
    :target: http://bioconda.github.io/recipes/gw/README.html
 
-.. image:: include/banner.png
+.. image:: include/resources/images/banner.png
     :align: center
 
 
@@ -100,7 +100,7 @@ To view a genomic region e.g. chr1:1-20000, supply an indexed reference genome a
 
     gw hg38 -b your.bam -r chr1:1-20000
 
-.. image:: include/chr1.png
+.. image:: include/resources/images/chr1.png
     :align: center
 
 
@@ -110,7 +110,7 @@ A variant file in .vcf/.bcf format can be opened in a GW window by either draggi
 
     gw hg38.fa -b your.bam -v variants.vcf
 
-.. image:: include/tiles.png
+.. image:: include/resources/images/tiles.png
     :align: center
 
 

diff --git a/docs/docs/guide/Alignments.md b/docs/docs/guide/Alignments.md
@@ -2,7 +2,7 @@
 title: Alignment data
 layout: home
 parent: User guide
-nav_order: 1
+nav_order: 3
 ---
 
 # Alignment data

diff --git a/docs/docs/guide/Commands.md b/docs/docs/guide/Commands.md
@@ -156,7 +156,8 @@ This is a shorthand for `filter flag & proper-pair`. For the inverse (keeping di
     filter ~proper-pair
 
 
-The `pattern` property can accept the values:
+The `pattern` property can accept the values `deletion`, `duplication`, `translocation`, `inversion_forward`, or
+`inversion_reverse`. These pattern can also be used with a shorthand name e.g.:
 
     filter pattern == del    # deletion pattern
     filter pattern == dup    # duplication pattern

diff --git a/docs/docs/guide/Genomes.md b/docs/docs/guide/Genomes.md
@@ -0,0 +1,35 @@
+---
+title: Genomes and Ideograms
+layout: home
+parent: User guide
+nav_order: 1
+---
+
+# Genomes
+
+
+
+
+# Ideograms
+
+
+Many of the reference genomes come with a preset ideogram and will be loaded automatically
+when a matching genome tag is used e.g. 'hg19' or 't2t' etc.
+
+To configure GW to use an ideogram for a genome tag add this to the 'tracks'
+section of settings (or your .gw.ini file)::
+
+    [tracks]
+    hg38_ideogram=path_to_ideogram.bed
+
+This will set the ideogram path for the 'hg38' genome tag. Once this has been saved
+in the settings menu, the ideogram will be loaded whenever the hg38 genome tag is used.
+For example, using the load command::
+
+    load genome hg38
+
+Or when using 'hg38' tag from the command line.
+
+The CLI interface also has the `--ideogram` option
+
+
diff --git a/docs/docs/guide/Hotkeys.md b/docs/docs/guide/Hotkeys.md
@@ -2,7 +2,7 @@
 title: Hot keys
 layout: home
 parent: User guide
-nav_order: 8
+nav_order: 10
 ---
 
 # Hot keys and shortcuts

diff --git a/docs/docs/guide/Image_tiles.md b/docs/docs/guide/Image_tiles.md
@@ -2,7 +2,7 @@
 title: Image tiles
 layout: home
 parent: User guide
-nav_order: 3
+nav_order: 5
 ---
 
 # Variant data and image tiles

diff --git a/docs/docs/guide/Images.md b/docs/docs/guide/Images.md
@@ -2,7 +2,7 @@
 title: Images
 layout: home
 parent: User guide
-nav_order: 6
+nav_order: 8
 ---
 
 # Images

diff --git a/docs/docs/guide/Labelling.md b/docs/docs/guide/Labelling.md
@@ -2,7 +2,7 @@
 title: Labelling
 layout: home
 parent: User guide
-nav_order: 4
+nav_order: 6
 ---
 
 # Labelling

diff --git a/docs/docs/guide/Remote.md b/docs/docs/guide/Remote.md
@@ -2,7 +2,7 @@
 title: Remote
 layout: home
 parent: User guide
-nav_order: 9
+nav_order: 11
 ---
 
 # Loading remote data

diff --git a/docs/docs/guide/Settings.md b/docs/docs/guide/Settings.md
@@ -2,7 +2,7 @@
 title: Settings
 layout: home
 parent: User guide
-nav_order: 7
+nav_order: 9
 ---
 
 # Settings and config
@@ -33,4 +33,10 @@ is defined as a comma-separated-list of paths. For example:
 hg19=a.bed,b.gff3
 ```
 
-This line will tell GW to load a bed file and a gff3 track file when the `hg19` genome-tag is used.
+This line will tell GW to load a bed file and a gff3 track file when the `hg19` genome-tag is used.
+
+Ideograms can be configured by appending `_ideogram` to the tag e.g.:
+
+```shell
+hg19_ideogram=hg19.ideogram.bed
+```
diff --git a/docs/docs/guide/Tracks.md b/docs/docs/guide/Tracks.md
@@ -2,7 +2,7 @@
 title: Tracks
 layout: home
 parent: User guide
-nav_order: 3
+nav_order: 7
 ---
 
 # Tracks

diff --git a/include/resources/cytobands/ce11.cytoBand.bed b/include/resources/cytobands/ce11.cytoBand.bed
@@ -0,0 +1,8 @@
+#chrom	chromStart	chromEnd	name	gieStain
+chrI	0	15072434		gneg
+chrM	0	13794		gneg
+chrV	0	20924180		gneg
+chrX	0	17718942		gneg
+chrII	0	15279421		gneg
+chrIV	0	17493829		gneg
+chrIII	0	13783801		gneg