@jbrowse/plugin-spreadsheet-view 2.6.1

package/src/SpreadsheetView/test_data/starfusion_example.fusion_predictions.tsv

@@ -0,0 +1,25 @@
+#FusionName	JunctionReadCount	SpanningFragCount	SpliceType	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	LargeAnchorSupport	FFPM	LeftBreakDinuc	LeftBreakEntropy	RightBreakDinuc	RightBreakEntropy	annots
+THRA--AC090627.1	27	93	ONLY_REF_SPLICE	THRA^ENSG00000126351.8	chr17:38243106:+	AC090627.1^ENSG00000235300.3	chr17:46371709:+	YES_LDAS	23875.8456	GT	1.8892	AG	1.9656	["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr17:8.12Mb]"]
+THRA--AC090627.1	5	93	ONLY_REF_SPLICE	THRA^ENSG00000126351.8	chr17:38243106:+	AC090627.1^ENSG00000235300.3	chr17:46384693:+	YES_LDAS	19498.6072	GT	1.8892	AG	1.4295	["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr17:8.12Mb]"]
+ACACA--STAC2	12	52	ONLY_REF_SPLICE	ACACA^ENSG00000132142.15	chr17:35479453:-	STAC2^ENSG00000141750.6	chr17:37374426:-	YES_LDAS	12733.7844	GT	1.9656	AG	1.9656	["ChimerSeq","CCLE","Klijn_CellLines","FA_CancerSupp","INTRACHROMOSOMAL[chr17:1.60Mb]"]
+RPS6KB1--SNF8	10	43	ONLY_REF_SPLICE	RPS6KB1^ENSG00000108443.9	chr17:57970686:+	SNF8^ENSG00000159210.5	chr17:47021337:-	YES_LDAS	10545.1651	GT	1.3753	AG	1.8323	["Klijn_CellLines","FA_CancerSupp","ChimerSeq","CCLE","INTRACHROMOSOMAL[chr17:10.95Mb]"]
+TOB1--SYNRG	8	30	ONLY_REF_SPLICE	TOB1^ENSG00000141232.4	chr17:48943419:-	SYNRG^ENSG00000006114.11	chr17:35880751:-	YES_LDAS	7560.6844	GT	1.4566	AG	1.8892	["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr17:12.97Mb]"]
+VAPB--IKZF3	4	46	ONLY_REF_SPLICE	VAPB^ENSG00000124164.11	chr20:56964573:+	IKZF3^ENSG00000161405.12	chr17:37934020:-	YES_LDAS	9948.269	GT	1.9656	AG	1.7819	["FA_CancerSupp","Klijn_CellLines","CCLE","ChimerSeq","ChimerPub","INTERCHROMOSOMAL[chr20--chr17]"]
+ZMYND8--CEP250	2	44	ONLY_REF_SPLICE	ZMYND8^ENSG00000101040.15	chr20:45852970:-	CEP250^ENSG00000126001.11	chr20:34078463:+	NO_LDAS	9152.4075	GT	1.8295	AG	1.8062	["FA_CancerSupp","CCLE","ChimerSeq","INTRACHROMOSOMAL[chr20:11.74Mb]"]
+AHCTF1--NAAA	3	38	ONLY_REF_SPLICE	AHCTF1^ENSG00000153207.10	chr1:247094880:-	NAAA^ENSG00000138744.10	chr4:76846964:-	YES_LDAS	8157.5805	GT	1.7232	AG	1.8062	["FA_CancerSupp","CCLE","INTERCHROMOSOMAL[chr1--chr4]"]
+VAPB--IKZF3	1	46	ONLY_REF_SPLICE	VAPB^ENSG00000124164.11	chr20:56964573:+	IKZF3^ENSG00000161405.12	chr17:37922746:-	NO_LDAS	9351.3729	GT	1.9656	AG	1.9329	["FA_CancerSupp","Klijn_CellLines","CCLE","ChimerSeq","ChimerPub","INTERCHROMOSOMAL[chr20--chr17]"]
+VAPB--IKZF3	1	46	ONLY_REF_SPLICE	VAPB^ENSG00000124164.11	chr20:56964573:+	IKZF3^ENSG00000161405.12	chr17:37944627:-	NO_LDAS	9351.3729	GT	1.9656	AG	1.8892	["FA_CancerSupp","Klijn_CellLines","CCLE","ChimerSeq","ChimerPub","INTERCHROMOSOMAL[chr20--chr17]"]
+STX16--RAE1	4	33	ONLY_REF_SPLICE	STX16^ENSG00000124222.17	chr20:57227143:+	RAE1^ENSG00000101146.8	chr20:55929088:+	YES_LDAS	7361.719	GT	1.9899	AG	1.9656	["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr20:1.27Mb]"]
+AHCTF1--NAAA	1	38	ONLY_REF_SPLICE	AHCTF1^ENSG00000153207.10	chr1:247094431:-	NAAA^ENSG00000138744.10	chr4:76846964:-	NO_LDAS	7759.6498	GT	1.9086	AG	1.8062	["FA_CancerSupp","CCLE","INTERCHROMOSOMAL[chr1--chr4]"]
+STX16-NPEPL1--RAE1	4	24	INCL_NON_REF_SPLICE	STX16-NPEPL1^ENSG00000254995.4	chr20:57227143:+	RAE1^ENSG00000101146.8	chr20:55929088:+	YES_LDAS	5571.0306	GT	1.9899	AG	1.9656	INTRACHROMOSOMAL[chr20:1.27Mb]
+RAB22A--MYO9B	6	11	ONLY_REF_SPLICE	RAB22A^ENSG00000124209.3	chr20:56886178:+	MYO9B^ENSG00000099331.9	chr19:17256207:+	YES_LDAS	3382.4115	GT	1.6895	AG	1.9656	["FA_CancerSupp","ChimerSeq","CCLE","INTERCHROMOSOMAL[chr20--chr19]"]
+MED1--ACSF2	4	11	ONLY_REF_SPLICE	MED1^ENSG00000125686.7	chr17:37595418:-	ACSF2^ENSG00000167107.8	chr17:48548389:+	YES_LDAS	2984.4807	GT	1.9656	AG	1.9656	["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr17:10.90Mb]"]
+MED13--BCAS3	2	12	ONLY_REF_SPLICE	MED13^ENSG00000108510.5	chr17:60129898:-	BCAS3^ENSG00000141376.16	chr17:59469338:+	YES_LDAS	2785.5154	GT	1.5546	AG	1.9086	["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr17:0.55Mb]"]
+MED1--STXBP4	1	15	ONLY_REF_SPLICE	MED1^ENSG00000125686.7	chr17:37607291:-	STXBP4^ENSG00000166263.9	chr17:53218671:+	NO_LDAS	3183.4461	GT	1.3996	AG	1.7968	["CCLE","FA_CancerSupp","Klijn_CellLines","INTRACHROMOSOMAL[chr17:15.44Mb]"]
+MED13--BCAS3	1	12	ONLY_REF_SPLICE	MED13^ENSG00000108510.5	chr17:60129898:-	BCAS3^ENSG00000141376.16	chr17:59465979:+	NO_LDAS	2586.55	GT	1.5546	AG	0.8366	["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr17:0.55Mb]"]
+STARD3--DOK5	2	7	ONLY_REF_SPLICE	STARD3^ENSG00000131748.11	chr17:37793484:+	DOK5^ENSG00000101134.7	chr20:53259997:+	NO_LDAS	1790.6885	GT	1.8892	AG	1.9656	["FA_CancerSupp","CCLE","INTERCHROMOSOMAL[chr17--chr20]"]
+DIDO1--TTI1	1	10	ONLY_REF_SPLICE	DIDO1^ENSG00000101191.12	chr20:61569148:-	TTI1^ENSG00000101407.8	chr20:36642259:-	NO_LDAS	2188.6192	GT	1.6402	AG	1.9329	["FA_CancerSupp","ChimerSeq","CCLE","INTRACHROMOSOMAL[chr20:24.85Mb]"]
+DIDO1--TTI1	1	10	ONLY_REF_SPLICE	DIDO1^ENSG00000101191.12	chr20:61569148:-	TTI1^ENSG00000101407.8	chr20:36634799:-	NO_LDAS	2188.6192	GT	1.6402	AG	1.8892	["FA_CancerSupp","ChimerSeq","CCLE","INTRACHROMOSOMAL[chr20:24.85Mb]"]
+BRD4--RFX1	1	8	ONLY_REF_SPLICE	BRD4^ENSG00000141867.13	chr19:15443101:-	RFX1^ENSG00000132005.4	chr19:14109129:-	NO_LDAS	1790.6884	GT	1.9086	AG	1.8892	["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr19:1.23Mb]"]
+BRD4--RFX1	1	8	ONLY_REF_SPLICE	BRD4^ENSG00000141867.13	chr19:15443101:-	RFX1^ENSG00000132005.4	chr19:14094407:-	NO_LDAS	1790.6884	GT	1.9086	AG	1.8295	["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr19:1.23Mb]"]
+TRPC4AP--MRPL45	1	8	ONLY_REF_SPLICE	TRPC4AP^ENSG00000100991.7	chr20:33665849:-	MRPL45^ENSG00000174100.5	chr17:36478009:+	NO_LDAS	1790.6884	GT	1.6895	AG	1.9086	["CCLE","Klijn_CellLines","FA_CancerSupp","INTERCHROMOSOMAL[chr20--chr17]"]

package/src/SpreadsheetView/test_data/volvox.sort.bed

@@ -0,0 +1,109 @@
+contigA	3000	3009
+contigA	3105	3114
+contigA	3152	3161
+contigA	3171	3180
+contigA	3174	3183
+contigA	3213	3222
+contigA	3465	3474
+contigA	3795	3804
+contigA	4035	4044
+contigA	4073	4082
+contigA	4074	4083
+contigA	4166	4175
+contigA	4179	4188
+contigA	4204	4213
+contigA	4248	4257
+contigA	4260	4269
+contigA	4577	4586
+contigA	4828	4837
+contigA	4901	4910
+contigA	5006	5015
+contigA	5051	5060
+contigA	5201	5210
+contigA	5260	5269
+contigA	5281	5290
+contigA	5349	5358
+contigA	5353	5362
+contigA	5423	5432
+contigA	5457	5466
+contigA	5548	5557
+contigA	5626	5635
+contigA	5835	5844
+contigA	5909	5918
+contigA	5927	5936
+contigA	5969	5978
+contigA	6070	6079
+contigA	6185	6194
+contigA	6285	6294
+contigA	6363	6372
+contigA	6559	6568
+contigA	6834	6843
+contigA	6908	6917
+contigA	6918	6927
+contigA	7141	7150
+contigA	7173	7182
+contigA	7569	7578
+contigA	7619	7628
+contigA	7654	7663
+contigA	7671	7680
+contigA	7707	7716
+contigA	7739	7748
+contigA	8077	8086
+contigA	8128	8137
+contigA	8132	8141
+contigA	8210	8219
+contigA	8267	8276
+contigA	8328	8337
+contigA	8524	8533
+contigA	8659	8668
+contigA	8660	8669
+contigA	8742	8751
+contigA	8811	8820
+contigA	8816	8825
+contigA	8964	8973
+contigA	9048	9057
+contigA	9054	9063
+contigA	9136	9145
+contigA	9243	9252
+contigA	9320	9329
+contigA	9366	9375
+contigA	9525	9534
+contigA	9580	9589
+contigA	9610	9619
+contigA	9744	9753
+contigA	9753	9762
+contigA	9759	9768
+contigA	9807	9816
+contigA	9853	9862
+contigA	9884	9893
+contigA	9920	9929
+contigA	10043	10052
+contigA	10216	10225
+contigA	10217	10226
+contigA	10252	10261
+contigA	10384	10393
+contigA	10498	10507
+contigA	10585	10594
+contigA	10684	10693
+contigA	10781	10790
+contigA	10875	10884
+contigA	11004	11013
+contigA	11095	11104
+contigA	11182	11191
+contigA	11207	11216
+contigA	11241	11250
+contigA	11335	11344
+contigA	11340	11349
+contigA	11535	11544
+contigA	11543	11552
+contigA	11549	11558
+contigA	11653	11662
+contigA	11675	11684
+contigA	11689	11698
+contigA	11774	11783
+contigA	11832	11841
+contigA	12386	12395
+contigA	12408	12417
+contigA	12441	12450
+contigA	12530	12539
+contigA	12738	12747

package/src/index.ts

@@ -0,0 +1,38 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import Plugin from '@jbrowse/core/Plugin'
+import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
+
+// icons
+import ViewComfyIcon from '@mui/icons-material/ViewComfy'
+
+// locals
+import SpreadsheetViewF from './SpreadsheetView'
+
+import LaunchSpreadsheetViewF from './LaunchSpreadsheetView'
+
+export default class SpreadsheetViewPlugin extends Plugin {
+  name = 'SpreadsheetViewPlugin'
+
+  install(pluginManager: PluginManager) {
+    SpreadsheetViewF(pluginManager)
+    LaunchSpreadsheetViewF(pluginManager)
+  }
+
+  configure(pluginManager: PluginManager) {
+    const { rootModel } = pluginManager
+    if (isAbstractMenuManager(rootModel)) {
+      rootModel.appendToSubMenu(['Add'], {
+        label: 'Spreadsheet view',
+        icon: ViewComfyIcon,
+        onClick: (session: AbstractSessionModel) => {
+          session.addView('SpreadsheetView', {})
+        },
+      })
+    }
+  }
+}
+
+export {
+  type SpreadsheetViewModel,
+  type SpreadsheetViewStateModel,
+} from './SpreadsheetView'