Removed fluid from container to shore up header component overflow.

.devcontainer/devcontainer.json

@@ -0,0 +1,24 @@
+{
+  "image": "quay.io/vgteam/vg:v1.49.0",
+  "forwardPorts": [3000, 3001],
+  "features": {
+    "ghcr.io/devcontainers/features/node:1": {},
+    "ghcr.io/devcontainers/features/git:1": {},
+    "ghcr.io/devcontainers-contrib/features/apt-get-packages:1": {"packages": "nano"},
+    "ghcr.io/devcontainers-contrib/features/bash-command:1": {
+      "command": "echo aWYgW1sgISAteiAiJHtHSVRIVUJfQ09ERVNQQUNFU19QT1JUX0ZPUldBUkRJTkdfRE9NQUlOfSIgXV0gOyB0aGVuIGV4cG9ydCBXRFNfU09DS0VUX0hPU1Q9IiR7Q09ERVNQQUNFX05BTUV9LTMwMDEuJHtHSVRIVUJfQ09ERVNQQUNFU19QT1JUX0ZPUldBUkRJTkdfRE9NQUlOfSI7IGV4cG9ydCBXRFNfU09DS0VUX1BPUlQ9NDQzOyBleHBvcnQgSE9TVD0wLjAuMC4wOyBleHBvcnQgSFRUUFM9dHJ1ZTsgZmkK | base64 --decode >>/etc/bash.bashrc # Line to tell Webpack dev server to ignore HOST and use the Github Codespace port forward if we are in a Codespace. Need to base64 here because double quotes cannot be escaped through the devcontainer build process."
+    }
+  },
+"postCreateCommand": ". ${NVM_DIR}/nvm.sh && nvm install",
+"portsAttributes": {
+	"3001": {
+		"label": "devserver",
+    "protocol": "https"
+	},
+  "3000": {
+    "label": "api",
+    "onAutoForward": "silent"
+  }
+}
+}
+

README.md

@@ -103,6 +103,12 @@ PATH=/<your_path_to_folder_with_vg>:$PATH
 ssh -N -L 3001:localhost:3001 <your username>@<your server>
 ```
 
+#### Setting Up a Visualization
+
+The application comes with pre-set demos that you can use to learn the tool's visual language and basic features.
+
+To set up a custom visualization of particular files, you will need to configure a set of "tracks" describing the files you want to visualize, using the "Configure Tracks" dialog in "custom (mounted files)" mode. For information on how to do this, click on the "?" help button, or [read the help documentation online](public/help/help.md).
+
 #### Adding Your Own Data
 
 - The vg files you want to visualize need to contain haplotype/path info. Generating visualizations for the graph itself only is not supported. In addition to the haplotype graph, you can optionally visualize aligned reads from a gam file.
@@ -131,18 +137,27 @@ That can sometimes up to 10-20 seconds.
 If you already know of regions/subgraphs that you will be looking at, you can pre-fetch the data in advance. 
 This will save some time during the interactive visualization, especially if there are a lot of regions to visualize.
 
+This is a 2 step process that involves creating the chunk and linking it to a bed file
+
+1. 
 The subgraphs need to be pre-fetched using `vg chunk` like shown in [`prepare_chunks.sh`](scripts/prepare_chunks.sh). For example:
 
 ```
-XG=mygraph.xg GAM=mygam.gam GBWT=mygraph.gbwt REGION=chr1:1-100 OUTDIR=chunk-chr1-1-100 ./prepare_chunks.sh
+./prepare_chunk.sh -x mygraph.xg -h mygraph.gbwt -r chr1:1-100 -o chunk-chr1-1-100 -g mygam1.gam -g mygam2.gam
 ```
 
+2.
 Then compile those regions in a BED file with two additional columns: 
 
 - a description of the region (column 4)
 - the path to the output directory of the chunk, `chunk-chr1-1-100` in the example above, (column 5). 
 
-See an example in [`cactus.bed`](exampleData/cactus.bed). 
+```
+ref	1	10	region one to ten	chunk-ref-1-20
+ref	10	20	region ten to twenty	chunk-ref-1-20
+```
+Note each column is seperated by tabs
+
 This BED file will be read if placed in the `dataPath` directory, like for other files to mount (see above).
 
 #### Development Mode

exampleData/cactus1-20.bed

@@ -0,0 +1,2 @@
+ref	1	10	region one to ten	chunk-ref-1-20
+ref	10	20	region ten to twenty	chunk-ref-1-20

exampleData/chunk-ref-1-20/chunk.vg

@@ -0,0 +1,122 @@
+VGó
+
+GT

+d
+`GGAAGTGTTTGCTACCAAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACGTATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTG
+d
+`GGGGGGCTAGGGAAGACCTAGTCCTTCCAACAGCTATAAACAGTCCTGGATAATGGGTTTATGAAAAACACTTTTTCTTCCTTCAGCAAGCAAAAT
+d
+`TATTTATGAAGCTGTATGGTTTCAGCAACAGGGAGCAAAGGAAAAAAATCACCTCAAAGAAAGCAACAGCTTCCTTCCTGGTGGGATCTGTCATTT
+d
+`TATAGATATGAAATATTCATGCCAGAGGTCTTATATTTTAAGAGGAATGGATTATATACCAGAGCTACAACAATAAACATTTTACTTATTACTAAT
+d
+`GAGGAATTAGAAGACTGTCTTTGGAAACCGGTTCTTGAAAATCTTCTGCTGTTTTAGAACACATTCTTTAGAAATCTAGCAAATATATCTCAGACT
+d
+`TTTAGAAATCTCTTCTAGTTTCATTTTCCTTTTTTTTTTTTTTTTTTTGAGCCACAGTCTCACTGTCACCCAGGCTGGAGTGCCGTGGTATGATCT
+d
+`TGGCTCACTGCAACCTCCACCTCCCGGGCTGAAGTGATTCTCCTGCCTTAGCCACCTGAGTAGCTGGGATTACAGGTGTCCACCACCATGACCGGC
+d
+`TAATTTCTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTTTCGAACTCCTGACCTCCAGTGATCTGCCCACCTTGGCCTCCC	
+d
+`AAAGTGCTGGGATTACAGGCGTGAGCCACCATGCCCAGGTTTCAAGTTTCCTTTTCATTTCTAATACCTGCCTCAGAATTTCCTCCCCAATGTTCC
+
+d
+`ACTCCAACATTTGAGAACTGCCCAAGGACTATTCTGACTTTAAGTCACATAATCGATCCCAAGCACTCTCCTTCCATTGAAGGGTCTGACTCTCTG
+d
+`CCTTTGTGAACACAGGGTTTTAGAGAAGTAAACTTAGGGAAACCAGCTATTCTCTTGAGGCCAAGCCACTCTGTGCTTCCAGCCCTAAGCCAACAA
+d
+`CAGCCTGAATAGAAAGAATAGGGCTGATAAATAATGAATCAGCATCTTGCTCAATTGGTGGCGTTTAAATGGTTTTAAAATCTTCTCAGGTGAAAA
+d
+`ATTACCATAATTTTGTGCTCATGGCAGATTTCCAAGGGAGACTTCAAGCAGAAAATCTTTAAGGGACCCTTGCATAGCCAGAAGTCCTTTTCAGGC
+d
+`TGATGTACATAAAATATTTAGTAGCCAGGACAGTAGAAGGACTGAAGAGTGAGAGGAGCTCCCAGGGCCTGGAAAGGCCACTTTGTAAGCTCATTC
+d
+`TTGGGGTCCTGTGGCTCTGTACCTGTGGCTGGCTGCAGTCAGTAGTGGCTGTGGGGGATCTGGGGTATCAGGTAGGTGTCCAGCTCCTGGCACTGG
+d
+`TAGAGTGCTACACTGTCCAACACCCACTCTCGGGTCACCACAGGTGCCTCACACATCTGCCCAATTGCTGGAGACAGAGAACACAAGCAGAGATTA
+d
+`GTGTCAATTCATTCTCCTGGACTAGGCTCTAATCAATCGACTCCAGGGTCCTGGTTGTATGAGTTCTTAGGATTAATGAGGTAGAAGCTAATTTTT
+d
+`TTTTTTTTTTTTTGAGACGGAGTCTTGCTCTGTCGCCGAGGCTAGAGTGTGATGGCGCAATCTCGGCTCATTCAACCTCCGCCTCCTGGGTTCAAG
+d
+`CAATTCTCCTGTCTCTGCCTCCTGAGTAGCTGGAATTACAGGCACATGCCATCACACCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGGTTTC
+d
+`ACAATGTTGGCCAGGCTGCTCTGGAACTCCTGACCTCAGGTGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCA
+
+CCTGG
		
+
+ä
+GI262359905[79264]
+ 
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exampleData/chunk-ref-1-20/chunk_contents.txt

@@ -0,0 +1,6 @@
+chunk-1_0_ref_0_1926.gam
+chunk.vg
+chunk_0_ref_0_1926.annotate.txt
+chunk_0_ref_0_1926.gam
+regions.tsv
+tracks.json

exampleData/chunk-ref-1-20/regions.tsv

@@ -0,0 +1 @@
+ref	0	1927	chunk-ref-1-20/chunk_0_ref_0_1926.gam	chunk-ref-1-20/chunk_0_ref_0_1926.annotate.txt

exampleData/chunk-ref-1-20/tracks.json

@@ -0,0 +1,8 @@
+{
+  "graph_file": "cactus.vg",
+  "haplotype_file": "",
+  "gam_files": [
+    "cactus0_10.sorted.gam",
+    "cactus10_20.sorted.gam"
+  ]
+}

exampleData/chunk-ref-2000-3000/chunk.vg

@@ -0,0 +1,162 @@
+VGô%
+g
+cAGACGGAGTCTTGCTCTTGTTGCTCAGCCTGGAATGCAATGGCACGATCTCAGCTCACTGCAACCTCCACCTCCCGGGTTCAAGCAATTCTCCTGCCTC
+g
+cAGCCTCCCAAGTAGCAGGGATTACAGGTGCCTGCCACCATGCCAGGCTAATTGTTTTTTCTTTTTTTTCAGATGGAGTCTCACTCTGTCACTCAGGCTG
+g
+cGATTGTGATGGTGTGATCTCAGCTCACTGCAACCTCAACATCCTGGGTTCAAGCGATTCTCCTGCCTCAGTCTCCCAAGTAGCTGGGACTACAAGTGCG
+g
+cTGCCACCATGCCTGGCTAATTTTTTTTAGTATTTTTAGTAGAGATGGGGTTTCGCCATATTGGCCAGGCTGGTCTCAAACTCCTGATGTCAGGTGATCC
+g
+cGCCCTGAGGCTGAGGCAGGAGAATCATTTAAACCCAGGAGGCGGAGGTTGCAGTGAGCCAAGACTGGGCCACTGCACTCCAGCCTGCTAAGTGACAGAG
+g
+cTGAGACTCCACCTCAAAAAAAAAAAAAAAAGGCAATGCTTCAGGACATAAGGCCTTGCTCTGAAGAGGCCCTAGGAGTGACTCCTGGTGACAGTGAAAG
+g
+cCCCACAGCCTCTGGCAACTGTATTAACATGAACTTCAATCTGTTAAAGGAAAGCCACCAGGAAAACAGCACTGTAATTTAACGATGTGGAAAAATGTAT 
+g
+cGTAATATCTTAAGGAAAAAAGCAAAACAGTGTAATTATGATCACATTTTATAAAATACACGTGTATATATACGCACATATGCCTGGTGGAGTTTTATGG!
+g
+cTGATCATCTCCAAGTGGTGGAATTACTGGGATTATTTTATTGTTTTTGTGTAAATTTATACTTTCTTTTTTCTTTTTGAGACACGGTCTCGCTCTGTCG"
+g
+cCCCAGGCTGGAGTACAGTGGTGTGATCGTGGCTCACTGAAGCATCAACCTCCTGAGCTCAAGTGATCCTCCCACCTCAGCTTCCCAAGTAGCTGCGACT#
+g
+cACAGGCATCTGCCACCACACCCAGCTACTTTTTAAATTTGTTGTACAGATGAAGTCTCCTTATGTTGCCCAGGCTGGTCTCGAACTTCTAGGCTCCCAC$
+g
+cCTTGACCTCCATCTTGACCTCCCAAAGTGCTGGAATTATAGGCATGAGCCACCATGCCCGGCCTTGATTTATGTTTTTGTGATGAACATTCATATCTTA%
+g
+cCTCCCACCCCATGGAAACAGTTCATGTATTACTTTTACAATATAAAACAAATAACAATAAAAACATCAAAAAGACATTTTAGCCATTCATTCAACAAAT&
+g
+cATTTAAAATGTGCCAAGAACTGTGCTACTCAAGCACCAGGTAATGAGTGATAAACCAAACCCATGCAAAAGGACCCCATATAGCACAGGTACATGCAGG'
+g
+cCACCTTACCATGGAAGCCATTGTCCTCTGTCCAGGCATCTGGCTGCACAACCACAATTGGGTGGACACCCTGGATCCCCAGGAAGGAAAGAGCATTCAA(
+g
+cAGTGTCAAAGTAGGACTACTGGAACTGTCACTTCATCATTTTTTTTGTTTGTTTTTGAGACAGGGTCTTGCTCTGTCACCCAGGCTGGAGTGCAGTGGT)
+g
+cGTGATCTCAGCTCACTGCCACCTCTGCCTCCTGGGCTCAAGCAATCCTTCCATCTCAGCCTCCTAAGTAGCTGGAACTACAGACACGTACCACCACCCC*
+g
+cTGGCTAATTTTTTTGTATTTTTGGTAGAGACAGGGTTTTGCCATGTTGCCCAGGCTGGTCTCAAACTCCTGGGCTCAACTTCACCCCCGGGATTATAGG+
+g
+cCATGAGCCACCGCACCCAGCCTTGGCTAATTTTTAATAATTTTTTTGTAGACATGAGGTCCTACTGTATTGCCCAGGCTGGTCTTCAGCTCCCAGGCTC,
+g
+cAAGCGATTCTCCCACCTTGGCCTCCCAGTGTTGTGATTACAGGGGTGGGGCACTGGCCCAGCCCATCATTTCTCTCTCTCTCTTTTTTTTTGAGACGGA-
+g
+cGTCTCGCTCTGTCGCCCGGGCTGGAGTGCAGTGGCGCGATCTTGGCTCACTGCAACCTCCGCCTCCGGGGTTCAAGCGATTCTCCTGCCCCAGCCCCTC.
+g
+cAAGTAGCTGGGACTACAGGCGTGCGCCCCTACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCGCCATGTTGGTTGGCCAGGATGGTCTC/
+g
+cGATCTCTTGACCTCGTGATCTGCCCACCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTAGCTTTTCTCTCTCTCTCTTTTTTT0
+g
+cTTTTTTTTAGACAAAGTCTCACTCTGTCACCCAGTCTGGAGTGCAGTGGTGCAATCTTGGCTCACTGCAACCTCTGCCTCCCACGTTCAAGCGATGCTC1
+g
+cACACCTCAACTTCCCAAATAGCTGGCATTACAGGCATGCTCCACCAGGCCTGGCTACTTTTTGTTTTTTTTTTTTTAGTACAGATGGGGTTTCACCATG2
+g
+cTTGGCCAGGCTGGTCTCAAACTCCTGACAAGTGATCCACCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGACATGAGCCACCATGCCCAGCCTCCAG3
+g
+cCCCATCATTTCTTGATGATTTGTTGAAACACAGTATGCTGGGGCAGTCACAGAGAGGAGGGGGAGGGACATATGGGAAAAAGAGTTAGAGGGAAAAAGT4
+g
+cCTTCCCTCAGTATATTTAATATGTGCAGTTCTCAAATCCTTACCCATCCCTTACAGATGGAGTCTTTTGGCACAGGTATGTGGGCAGAGAAGACTTCTG5
+g
+cAGGCTACAGTAGGGGCATCCATAGGGACTGACAGGTGCCAGTCTTGCTCACAGGAGAGAATATTGTGTCCTCCCTCTCTGACAGGGCACCCAATACTTA6
+g
+cCTGTGCCAAGGGTGAATGATGAAAGCTCCTTCACCACAGAAGCACCACACAGCTGTACCATCCATTCCAGTTGATCTAAAATGGACATTTAGATGTAAA7
+g
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exampleData/chunk-ref-2000-3000/regions.tsv

@@ -0,0 +1 @@
+ref	1955	5024	chunk-ref-2000-3000/chunk_0_ref_1955_5023.gam	chunk-ref-2000-3000/chunk_0_ref_1955_5023.annotate.txt

exampleData/chunk-ref-2000-3000/tracks.json

@@ -0,0 +1,7 @@
+{
+  "graph_file": "cactus.vg",
+  "haplotype_file": "",
+  "gam_files": [
+    "cactus-NA12879.sorted.gam"
+  ]
+}