@jbrowse/bandage-core 6.0.1 → 6.0.2

package/dist/cli/figure.js

@@ -1,27 +1,94 @@
 #!/usr/bin/env node
 import {
-  HPRC_GBZ,
-  LAYOUT_MODES,
-  cutGbzRegion,
-  featuresOnBackbone,
-  figureSvg,
-  filterSamples,
-  forceLayout,
   genesFromBed,
   genesFromGff3Lines,
-  genesFromText,
+  genesFromText
+} from "../chunks/chunk-BXEPA4KS.js";
+import {
+  LAYOUT_MODES,
+  layoutModeByValue
+} from "../chunks/chunk-527AI7CP.js";
+import "../chunks/chunk-P7B3GDAY.js";
+import "../chunks/chunk-TEDQJPMI.js";
+import "../chunks/chunk-LOEA5IHZ.js";
+import "../chunks/chunk-L3O7AWLI.js";
+import "../chunks/chunk-TZFWUT2C.js";
+import "../chunks/chunk-HNQPEMYE.js";
+import "../chunks/chunk-C44YRP5F.js";
+import "../chunks/chunk-RVS2QCOX.js";
+import {
+  loadBandage
+} from "../chunks/chunk-7XHHVYG7.js";
+import {
+  figureSvg
+} from "../chunks/chunk-CZ54VG2H.js";
+import "../chunks/chunk-47DYCZOK.js";
+import "../chunks/chunk-MHGHYHTL.js";
+import {
   genesOnRow,
-  graphBackbone,
+  placeRowGenes
+} from "../chunks/chunk-QCYM44UL.js";
+import "../chunks/chunk-D3M7SBKL.js";
+import "../chunks/chunk-SV27AJCC.js";
+import "../chunks/chunk-3S3YVOJ7.js";
+import "../chunks/chunk-KCW7L3NV.js";
+import "../chunks/chunk-L5RYUPZI.js";
+import "../chunks/chunk-6Q6HFBJT.js";
+import "../chunks/chunk-IMW3AK27.js";
+import "../chunks/chunk-AE3UQZY3.js";
+import {
+  forceLayout,
+  loadGraph
+} from "../chunks/chunk-VKB57ZYE.js";
+import "../chunks/chunk-PUG7LXDF.js";
+import "../chunks/chunk-IGVV37VI.js";
+import "../chunks/chunk-72N5DJHZ.js";
+import "../chunks/chunk-QYBZZI5H.js";
+import "../chunks/chunk-CDLPYR5O.js";
+import "../chunks/chunk-MI35EUIE.js";
+import "../chunks/chunk-5QT6NPSO.js";
+import "../chunks/chunk-3WHKR5TY.js";
+import "../chunks/chunk-MNUSQCLG.js";
+import "../chunks/chunk-HB6PDCOU.js";
+import "../chunks/chunk-BJV2W4KZ.js";
+import "../chunks/chunk-LVZZH2NI.js";
+import "../chunks/chunk-6YRRNX2P.js";
+import "../chunks/chunk-EZPBJPK6.js";
+import {
+  filterSamples,
+  walkRows
+} from "../chunks/chunk-SZNZ2T6D.js";
+import "../chunks/chunk-7CHJKABZ.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-HCANBJDD.js";
+import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-SDGM243E.js";
+import "../chunks/chunk-PBENCR5L.js";
+import "../chunks/chunk-UVBGRJQX.js";
+import "../chunks/chunk-6JEWNXCQ.js";
+import "../chunks/chunk-JKJWSY4V.js";
+import "../chunks/chunk-X32PABB7.js";
+import "../chunks/chunk-3PLYZLYV.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-NNODIW4U.js";
+import "../chunks/chunk-6SBUFFTB.js";
+import {
+  HPRC_GBZ,
+  cutGbzRegion,
   haplotypeIndexBeside,
-  layoutModeByValue,
-  loadBandage,
-  loadGraph,
   openGbz,
-  parseRegion,
-  placeRowGenes,
-  refNameBinding,
-  walkRows
-} from "../chunks/chunk-EXSFRX2F.js";
+  parseRegion
+} from "../chunks/chunk-73RSLGZT.js";
+import "../chunks/chunk-LTUWJKHD.js";
+import "../chunks/chunk-WSIFAZU7.js";
+import {
+  featuresOnBackbone,
+  graphBackbone,
+  refNameBinding
+} from "../chunks/chunk-RAKOB6IV.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-FYQWPEEY.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";

package/dist/colorSchemes.js

@@ -0,0 +1,10 @@
+import {
+  COLOR_SCHEMES,
+  COLOR_SCHEME_VALUES,
+  resolveColorScheme
+} from "./chunks/chunk-JKJWSY4V.js";
+export {
+  COLOR_SCHEMES,
+  COLOR_SCHEME_VALUES,
+  resolveColorScheme
+};

package/dist/deletionEdges.js

@@ -0,0 +1,13 @@
+import {
+  bypassedPoints,
+  deletionArcCurves,
+  deletionEdges
+} from "./chunks/chunk-X32PABB7.js";
+import "./chunks/chunk-3PLYZLYV.js";
+import "./chunks/chunk-CPMHA4W5.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  bypassedPoints,
+  deletionArcCurves,
+  deletionEdges
+};

package/dist/el.js

@@ -0,0 +1,8 @@
+import {
+  el,
+  serializeEl
+} from "./chunks/chunk-NNODIW4U.js";
+export {
+  el,
+  serializeEl
+};

package/dist/facetGrid.js

@@ -0,0 +1,16 @@
+import {
+  FACET_GAP_PX,
+  FACET_PAD_PX,
+  FACET_TITLE_PX,
+  facetCells,
+  facetGrid,
+  facetSettingOf
+} from "./chunks/chunk-6SBUFFTB.js";
+export {
+  FACET_GAP_PX,
+  FACET_PAD_PX,
+  FACET_TITLE_PX,
+  facetCells,
+  facetGrid,
+  facetSettingOf
+};

package/dist/figure.js

@@ -0,0 +1,51 @@
+import {
+  figureSvg
+} from "./chunks/chunk-CZ54VG2H.js";
+import "./chunks/chunk-47DYCZOK.js";
+import "./chunks/chunk-MHGHYHTL.js";
+import "./chunks/chunk-QCYM44UL.js";
+import "./chunks/chunk-D3M7SBKL.js";
+import "./chunks/chunk-SV27AJCC.js";
+import "./chunks/chunk-3S3YVOJ7.js";
+import "./chunks/chunk-KCW7L3NV.js";
+import "./chunks/chunk-L5RYUPZI.js";
+import "./chunks/chunk-6Q6HFBJT.js";
+import "./chunks/chunk-IMW3AK27.js";
+import "./chunks/chunk-AE3UQZY3.js";
+import "./chunks/chunk-VKB57ZYE.js";
+import "./chunks/chunk-PUG7LXDF.js";
+import "./chunks/chunk-IGVV37VI.js";
+import "./chunks/chunk-72N5DJHZ.js";
+import "./chunks/chunk-QYBZZI5H.js";
+import "./chunks/chunk-CDLPYR5O.js";
+import "./chunks/chunk-MI35EUIE.js";
+import "./chunks/chunk-5QT6NPSO.js";
+import "./chunks/chunk-3WHKR5TY.js";
+import "./chunks/chunk-MNUSQCLG.js";
+import "./chunks/chunk-HB6PDCOU.js";
+import "./chunks/chunk-BJV2W4KZ.js";
+import "./chunks/chunk-LVZZH2NI.js";
+import "./chunks/chunk-6YRRNX2P.js";
+import "./chunks/chunk-EZPBJPK6.js";
+import "./chunks/chunk-SZNZ2T6D.js";
+import "./chunks/chunk-7CHJKABZ.js";
+import "./chunks/chunk-ST2IBUAN.js";
+import "./chunks/chunk-ES2N6V56.js";
+import "./chunks/chunk-HCANBJDD.js";
+import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-SDGM243E.js";
+import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-UVBGRJQX.js";
+import "./chunks/chunk-6JEWNXCQ.js";
+import "./chunks/chunk-JKJWSY4V.js";
+import "./chunks/chunk-X32PABB7.js";
+import "./chunks/chunk-3PLYZLYV.js";
+import "./chunks/chunk-CPMHA4W5.js";
+import "./chunks/chunk-NNODIW4U.js";
+import "./chunks/chunk-6SBUFFTB.js";
+import "./chunks/chunk-RAKOB6IV.js";
+import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  figureSvg
+};

package/dist/gaf/parseGaf.js

@@ -0,0 +1,12 @@
+import {
+  parseCs,
+  parseGaf,
+  parseGafLine,
+  parseGafPath
+} from "../chunks/chunk-C44YRP5F.js";
+export {
+  parseCs,
+  parseGaf,
+  parseGafLine,
+  parseGafPath
+};

package/dist/gbzCut.js

@@ -0,0 +1,19 @@
+import {
+  HPRC_GBZ,
+  cutGbzRegion,
+  haplotypeIndexBeside,
+  openGbz,
+  parseRegion
+} from "./chunks/chunk-73RSLGZT.js";
+import "./chunks/chunk-LTUWJKHD.js";
+import "./chunks/chunk-WSIFAZU7.js";
+import "./chunks/chunk-RAKOB6IV.js";
+import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  HPRC_GBZ,
+  cutGbzRegion,
+  haplotypeIndexBeside,
+  openGbz,
+  parseRegion
+};

package/dist/gbzJoin.js

@@ -0,0 +1,6 @@
+import {
+  joinCuts
+} from "./chunks/chunk-WSIFAZU7.js";
+export {
+  joinCuts
+};

package/dist/gbzWindow.js

@@ -0,0 +1,28 @@
+import {
+  GBZ_CUT_DEFAULTS,
+  NoReferenceSampleError,
+  NodeLimitError,
+  cutWindowGFA,
+  haplotypePrefix,
+  haplotypeWanted,
+  nodeLimitError,
+  referencePathQuery,
+  referenceSamplesOf,
+  resolveReferenceSample
+} from "./chunks/chunk-LTUWJKHD.js";
+import "./chunks/chunk-WSIFAZU7.js";
+import "./chunks/chunk-RAKOB6IV.js";
+import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  GBZ_CUT_DEFAULTS,
+  NoReferenceSampleError,
+  NodeLimitError,
+  cutWindowGFA,
+  haplotypePrefix,
+  haplotypeWanted,
+  nodeLimitError,
+  referencePathQuery,
+  referenceSamplesOf,
+  resolveReferenceSample
+};

package/dist/genes/exonOutline.js

@@ -0,0 +1,11 @@
+import {
+  EXON_COLOR,
+  exonOutlineTree,
+  exonStretches
+} from "../chunks/chunk-3S3YVOJ7.js";
+import "../chunks/chunk-NNODIW4U.js";
+export {
+  EXON_COLOR,
+  exonOutlineTree,
+  exonStretches
+};

package/dist/genes/geneFiles.js

@@ -0,0 +1,14 @@
+import {
+  genesFromBed,
+  genesFromGff3Lines,
+  genesFromText,
+  mergeOverlappingByName,
+  mergedIntervals
+} from "../chunks/chunk-BXEPA4KS.js";
+export {
+  genesFromBed,
+  genesFromGff3Lines,
+  genesFromText,
+  mergeOverlappingByName,
+  mergedIntervals
+};

package/dist/genes/genePins.js

@@ -0,0 +1,10 @@
+import {
+  genePins
+} from "../chunks/chunk-SV27AJCC.js";
+import "../chunks/chunk-SDGM243E.js";
+import "../chunks/chunk-3PLYZLYV.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  genePins
+};

package/dist/gfa/gfaConverter.js

@@ -0,0 +1,11 @@
+import {
+  convertGFAToGraph
+} from "../chunks/chunk-72N5DJHZ.js";
+import "../chunks/chunk-QYBZZI5H.js";
+import "../chunks/chunk-CDLPYR5O.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  convertGFAToGraph
+};

package/dist/gfa-core/gfaParser.js

@@ -0,0 +1,8 @@
+import {
+  parseGFA,
+  stableCoordinate
+} from "../chunks/chunk-CDLPYR5O.js";
+export {
+  parseGFA,
+  stableCoordinate
+};

package/dist/gfa-core/index.js

@@ -0,0 +1,9 @@
+import "../chunks/chunk-QYBZZI5H.js";
+import {
+  parseGFA,
+  stableCoordinate
+} from "../chunks/chunk-CDLPYR5O.js";
+export {
+  parseGFA,
+  stableCoordinate
+};

package/dist/graphLabels.js

@@ -0,0 +1,24 @@
+import {
+  formatBp,
+  graphLabels,
+  groupDigits,
+  nodeLabelBudget,
+  placeSizeLabels,
+  rowLabelBox,
+  sizeLabelCandidates
+} from "./chunks/chunk-HCANBJDD.js";
+import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-SDGM243E.js";
+import "./chunks/chunk-X32PABB7.js";
+import "./chunks/chunk-3PLYZLYV.js";
+import "./chunks/chunk-CPMHA4W5.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  formatBp,
+  graphLabels,
+  groupDigits,
+  nodeLabelBudget,
+  placeSizeLabels,
+  rowLabelBox,
+  sizeLabelCandidates
+};