@jbrowse/plugin-alignments 2.2.2 → 2.3.1

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -34,7 +34,7 @@ const util_1 = require("@jbrowse/core/util");
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const clone_1 = __importDefault(require("clone"));
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
-const MismatchParser_1 = require("../BamAdapter/MismatchParser");
+const MismatchParser_1 = require("../MismatchParser");
 const useStyles = (0, mui_1.makeStyles)()({
     compact: {
         paddingRight: 0,

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map

@@ -1 +1 @@
-{"version":3,"file":"AlignmentsFeatureDetail.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,4CAOsB;AACtB,uCAA0C;AAC1C,2CAAqC;AACrC,6CAA+C;AAC/C,0EAAoC;AACpC,kDAAyB;AACzB,yFAI0D;AAC1D,iEAAyD;AAEzD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,OAAO,EAAE;QACP,YAAY,EAAE,CAAC;QACf,UAAU,EAAE,CAAC;QACb,aAAa,EAAE,CAAC;KACjB;CACF,CAAC,CAAA;AAEF,MAAM,IAAI,GAAG,CAAC,SAAS,EAAE,OAAO,CAAC,CAAA;AAEjC,8DAA8D;AAC9D,SAAS,cAAc,CAAC,KAAuB;IAC7C,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACzB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAA;IACzB,MAAM,SAAS,GAAG;QAChB,aAAa;QACb,4BAA4B;QAC5B,eAAe;QACf,eAAe;QACf,qBAAqB;QACrB,qBAAqB;QACrB,eAAe;QACf,gBAAgB;QAChB,uBAAuB;QACvB,2CAA2C;QAC3C,kCAAkC;QAClC,yBAAyB;KAC1B,CAAA;IACD,OAAO,CACL,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,OAAO;QAChC,8BAAC,+BAAW,IAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,GAAI;QAE3C,8BAAC,oBAAS,QACP,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE;YAC7B,MAAM,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAA;YAChC,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,8BAAC,2BAAgB,IACf,GAAG,EAAE,GAAG,EACR,OAAO,EACL,8BAAC,mBAAQ,IACP,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,IAAI,EAAE,IAAI,EACV,QAAQ,SACR,EAEJ,KAAK,EAAE,IAAI,GACX,CACH,CAAA;QACH,CAAC,CAAC,CACQ,CACH,CACZ,CAAA;AACH,CAAC;AAED,SAAS,SAAS,CAAC,EAAE,KAAK,EAAsB;IAC9C,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACvC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,OAAO,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC7B,IAAI,OAAO,CAAC,MAAM,GAAG,GAAG,EAAE;QACxB,OAAO,CACL;YACE,0CACE,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAA,2BAAI,EAAC,OAAO,CAAC,CAAA;oBACb,SAAS,CAAC,IAAI,CAAC,CAAA;oBACf,UAAU,CAAC,GAAG,EAAE;wBACd,SAAS,CAAC,KAAK,CAAC,CAAA;oBAClB,CAAC,EAAE,GAAG,CAAC,CAAA;gBACT,CAAC,IAEA,MAAM,CAAC,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,MAAM,CACjC;YACT,0CAAQ,IAAI,EAAC,QAAQ,EAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,IACtD,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,WAAW,CAC1B;YACT,2CAAM,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,CAAO,CAC1D,CACJ,CAAA;KACF;IACD,OAAO,2CAAM,OAAO,CAAO,CAAA;AAC7B,CAAC;AAED,yDAAyD;AACzD,SAAS,cAAc,CAAC,KAAa;IACnC,MAAM,QAAQ,GAAG,IAAA,2BAAU,EAAC,KAAK,CAAC,CAAA;IAClC,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QAC3C,MAAM,GAAG,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QACxB,MAAM,EAAE,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;QAC1B,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;YAC1C,WAAW,IAAI,GAAG,CAAA;SACnB;KACF;IACD,OAAO,WAAW,CAAA;AACpB,CAAC;AAED,8DAA8D;AAC9D,SAAS,uBAAuB,CAAC,KAAkC;IACjE,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAC5B,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,OAAO,CACL,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,0BAA0B;QACnD,8BAAC,qBAAU,oDAAuD;QAClE,0CACG,GAAG;aACD,KAAK,CAAC,GAAG,CAAC;aACV,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;aAClB,GAAG,CAAC,CAAC,EAAE,EAAE,KAAK,EAAE,EAAE;YACjB,MAAM,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;YACzD,MAAM,QAAQ,GAAG,cAAc,CAAC,OAAO,CAAC,CAAA;YACxC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,GAAG,CAAC,CAAC,CAAA;YACtC,MAAM,KAAK,GAAG,CAAC,OAAO,CAAA;YACtB,MAAM,GAAG,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAA;YAC/B,MAAM,SAAS,GAAG,GAAG,KAAK,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC,IACtD,GAAG,GAAG,KACR,EAAE,CAAA;YACF,MAAM,YAAY,GAAG,KAAK,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;YAClD,MAAM,UAAU,GAAG,GAAG,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;YAC9C,MAAM,aAAa,GAAG,GAAG,KAAK,IAAI,YAAY,IAAI,UAAU,KAAK,QAAQ,GAAG,CAAA;YAC5E,OAAO,CACL,sCAAI,GAAG,EAAE,GAAG,SAAS,IAAI,KAAK,EAAE;gBAC9B,8BAAC,eAAI,IACH,OAAO,EAAE,KAAK,EAAC,KAAK,EAAC,EAAE;wBACrB,KAAK,CAAC,cAAc,EAAE,CAAA;wBACtB,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;wBACtB,IAAI;4BACF,IAAI,IAAI,EAAE;gCACR,MAAM,IAAI,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;6BACrC;iCAAM;gCACL,MAAM,IAAI,KAAK,CACb,2CAA2C,CAC5C,CAAA;6BACF;yBACF;wBAAC,OAAO,CAAC,EAAE;4BACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;yBACvB;oBACH,CAAC,EACD,IAAI,EAAC,GAAG,IAEP,aAAa,CACT,CACJ,CACN,CAAA;QACH,CAAC,CAAC,CACD,CACI,CACZ,CAAA;AACH,CAAC;AAED,8DAA8D;AAC9D,SAAS,QAAQ,CAAC,EAAE,SAAS,EAAE,KAAK,EAAqC;IACvE,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,OAAO,CACL,8BAAC,eAAI,IACH,OAAO,EAAE,KAAK,IAAI,EAAE;YAClB,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;YACtB,IAAI,CAAC,IAAI,EAAE;gBACT,MAAM,IAAI,KAAK,CACb,2DAA2D,CAC5D,CAAA;aACF;YACD,IAAI;gBACF,MAAM,IAAI,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;aACrC;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;aACvB;QACH,CAAC,EACD,IAAI,EAAC,GAAG,IAEP,SAAS,CACL,CACR,CAAA;AACH,CAAC;AAED,8DAA8D;AAC9D,SAAS,uBAAuB,CAAC,KAAqB;IACpD,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,IAAI,GAAG,IAAA,eAAK,EAAC,KAAK,CAAC,WAAW,CAAC,CAAA;IACrC,MAAM,EAAE,GAAG,CAAC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,IAAI,CAAC,EAAE,CAAA;IACjD,OAAO,CACL,8BAAC,gBAAK,mBAAa,uBAAuB;QACxC,8BAAC,kCAAc,OACT,KAAK,EACT,IAAI,EAAE,IAAI,EACV,OAAO,EAAE,IAAI,EACb,SAAS,EAAE,CAAC,KAAK,EAAE,GAAG,EAAE,EAAE;gBACxB,OAAO,GAAG,KAAK,uBAAuB,CAAC,CAAC,CAAC,CACvC,8BAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,KAAe,GAAI,CACvD,CAAC,CAAC,CAAC,CACF,8BAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CAC5B,CAAA;YACH,CAAC,GACD;QACD,EAAE,CAAC,CAAC,CAAC,8BAAC,uBAAuB,IAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,GAAI,CAAC,CAAC,CAAC,IAAI;QAC9D,IAAI,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAC1B,8BAAC,cAAc,IAAC,OAAO,EAAE,IAAI,KAAM,KAAK,GAAI,CAC7C,CAAC,CAAC,CAAC,IAAI,CACF,CACT,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,uBAAuB,CAAC,CAAA"}
+{"version":3,"file":"AlignmentsFeatureDetail.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,4CAOsB;AACtB,uCAA0C;AAC1C,2CAAqC;AACrC,6CAA+C;AAC/C,0EAAoC;AACpC,kDAAyB;AACzB,yFAI0D;AAC1D,sDAA8C;AAE9C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,OAAO,EAAE;QACP,YAAY,EAAE,CAAC;QACf,UAAU,EAAE,CAAC;QACb,aAAa,EAAE,CAAC;KACjB;CACF,CAAC,CAAA;AAEF,MAAM,IAAI,GAAG,CAAC,SAAS,EAAE,OAAO,CAAC,CAAA;AAEjC,8DAA8D;AAC9D,SAAS,cAAc,CAAC,KAAuB;IAC7C,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACzB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAA;IACzB,MAAM,SAAS,GAAG;QAChB,aAAa;QACb,4BAA4B;QAC5B,eAAe;QACf,eAAe;QACf,qBAAqB;QACrB,qBAAqB;QACrB,eAAe;QACf,gBAAgB;QAChB,uBAAuB;QACvB,2CAA2C;QAC3C,kCAAkC;QAClC,yBAAyB;KAC1B,CAAA;IACD,OAAO,CACL,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,OAAO;QAChC,8BAAC,+BAAW,IAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,GAAI;QAE3C,8BAAC,oBAAS,QACP,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE;YAC7B,MAAM,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAA;YAChC,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,8BAAC,2BAAgB,IACf,GAAG,EAAE,GAAG,EACR,OAAO,EACL,8BAAC,mBAAQ,IACP,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,IAAI,EAAE,IAAI,EACV,QAAQ,SACR,EAEJ,KAAK,EAAE,IAAI,GACX,CACH,CAAA;QACH,CAAC,CAAC,CACQ,CACH,CACZ,CAAA;AACH,CAAC;AAED,SAAS,SAAS,CAAC,EAAE,KAAK,EAAsB;IAC9C,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACvC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,OAAO,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC7B,IAAI,OAAO,CAAC,MAAM,GAAG,GAAG,EAAE;QACxB,OAAO,CACL;YACE,0CACE,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAA,2BAAI,EAAC,OAAO,CAAC,CAAA;oBACb,SAAS,CAAC,IAAI,CAAC,CAAA;oBACf,UAAU,CAAC,GAAG,EAAE;wBACd,SAAS,CAAC,KAAK,CAAC,CAAA;oBAClB,CAAC,EAAE,GAAG,CAAC,CAAA;gBACT,CAAC,IAEA,MAAM,CAAC,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,MAAM,CACjC;YACT,0CAAQ,IAAI,EAAC,QAAQ,EAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,IACtD,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,WAAW,CAC1B;YACT,2CAAM,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,CAAO,CAC1D,CACJ,CAAA;KACF;IACD,OAAO,2CAAM,OAAO,CAAO,CAAA;AAC7B,CAAC;AAED,yDAAyD;AACzD,SAAS,cAAc,CAAC,KAAa;IACnC,MAAM,QAAQ,GAAG,IAAA,2BAAU,EAAC,KAAK,CAAC,CAAA;IAClC,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QAC3C,MAAM,GAAG,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QACxB,MAAM,EAAE,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;QAC1B,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;YAC1C,WAAW,IAAI,GAAG,CAAA;SACnB;KACF;IACD,OAAO,WAAW,CAAA;AACpB,CAAC;AAED,8DAA8D;AAC9D,SAAS,uBAAuB,CAAC,KAAkC;IACjE,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAC5B,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,OAAO,CACL,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,0BAA0B;QACnD,8BAAC,qBAAU,oDAAuD;QAClE,0CACG,GAAG;aACD,KAAK,CAAC,GAAG,CAAC;aACV,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;aAClB,GAAG,CAAC,CAAC,EAAE,EAAE,KAAK,EAAE,EAAE;YACjB,MAAM,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;YACzD,MAAM,QAAQ,GAAG,cAAc,CAAC,OAAO,CAAC,CAAA;YACxC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,GAAG,CAAC,CAAC,CAAA;YACtC,MAAM,KAAK,GAAG,CAAC,OAAO,CAAA;YACtB,MAAM,GAAG,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAA;YAC/B,MAAM,SAAS,GAAG,GAAG,KAAK,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC,IACtD,GAAG,GAAG,KACR,EAAE,CAAA;YACF,MAAM,YAAY,GAAG,KAAK,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;YAClD,MAAM,UAAU,GAAG,GAAG,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;YAC9C,MAAM,aAAa,GAAG,GAAG,KAAK,IAAI,YAAY,IAAI,UAAU,KAAK,QAAQ,GAAG,CAAA;YAC5E,OAAO,CACL,sCAAI,GAAG,EAAE,GAAG,SAAS,IAAI,KAAK,EAAE;gBAC9B,8BAAC,eAAI,IACH,OAAO,EAAE,KAAK,EAAC,KAAK,EAAC,EAAE;wBACrB,KAAK,CAAC,cAAc,EAAE,CAAA;wBACtB,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;wBACtB,IAAI;4BACF,IAAI,IAAI,EAAE;gCACR,MAAM,IAAI,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;6BACrC;iCAAM;gCACL,MAAM,IAAI,KAAK,CACb,2CAA2C,CAC5C,CAAA;6BACF;yBACF;wBAAC,OAAO,CAAC,EAAE;4BACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;yBACvB;oBACH,CAAC,EACD,IAAI,EAAC,GAAG,IAEP,aAAa,CACT,CACJ,CACN,CAAA;QACH,CAAC,CAAC,CACD,CACI,CACZ,CAAA;AACH,CAAC;AAED,8DAA8D;AAC9D,SAAS,QAAQ,CAAC,EAAE,SAAS,EAAE,KAAK,EAAqC;IACvE,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,OAAO,CACL,8BAAC,eAAI,IACH,OAAO,EAAE,KAAK,IAAI,EAAE;YAClB,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;YACtB,IAAI,CAAC,IAAI,EAAE;gBACT,MAAM,IAAI,KAAK,CACb,2DAA2D,CAC5D,CAAA;aACF;YACD,IAAI;gBACF,MAAM,IAAI,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;aACrC;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;aACvB;QACH,CAAC,EACD,IAAI,EAAC,GAAG,IAEP,SAAS,CACL,CACR,CAAA;AACH,CAAC;AAED,8DAA8D;AAC9D,SAAS,uBAAuB,CAAC,KAAqB;IACpD,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,IAAI,GAAG,IAAA,eAAK,EAAC,KAAK,CAAC,WAAW,CAAC,CAAA;IACrC,MAAM,EAAE,GAAG,CAAC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,IAAI,CAAC,EAAE,CAAA;IACjD,OAAO,CACL,8BAAC,gBAAK,mBAAa,uBAAuB;QACxC,8BAAC,kCAAc,OACT,KAAK,EACT,IAAI,EAAE,IAAI,EACV,OAAO,EAAE,IAAI,EACb,SAAS,EAAE,CAAC,KAAK,EAAE,GAAG,EAAE,EAAE;gBACxB,OAAO,GAAG,KAAK,uBAAuB,CAAC,CAAC,CAAC,CACvC,8BAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,KAAe,GAAI,CACvD,CAAC,CAAC,CAAC,CACF,8BAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CAC5B,CAAA;YACH,CAAC,GACD;QACD,EAAE,CAAC,CAAC,CAAC,8BAAC,uBAAuB,IAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,GAAI,CAAC,CAAC,CAAC,IAAI;QAC9D,IAAI,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAC1B,8BAAC,cAAc,IAAC,OAAO,EAAE,IAAI,KAAM,KAAK,GAAI,CAC7C,CAAC,CAAC,CAAC,IAAI,CACF,CACT,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,uBAAuB,CAAC,CAAA"}

package/dist/AlignmentsTrack/index.js

@@ -24,6 +24,7 @@ function register(pm) {
         const configSchema = configSchemaFactory(pm);
         const track = new TrackType_1.default({
             name: 'AlignmentsTrack',
+            displayName: 'Alignments track',
             configSchema,
             stateModel: (0, models_1.createBaseTrackModel)(pm, 'AlignmentsTrack', configSchema),
         });

package/dist/AlignmentsTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,+DAAiE;AACjE,uEAGmD;AAEnD;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,IAAA,mCAAmB,EACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,8BAAqB,EAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AACD,SAAwB,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,IAAI,mBAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AAfD,2BAeC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,+DAAiE;AACjE,uEAGmD;AAEnD;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,IAAA,mCAAmB,EACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,8BAAqB,EAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AACD,SAAwB,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,IAAI,mBAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AAhBD,2BAgBC"}

package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -13,9 +13,8 @@ export default class BamSlightlyLazyFeature implements Feature {
     _get_flags(): string;
     _get_strand(): number;
     _get_pair_orientation(): string | null | undefined;
-    _get_next_seq_id(): number;
-    _get_seq_id(): number;
-    _get_next_refName(): string | undefined;
+    _get_next_ref(): string | undefined;
+    _get_next_pos(): number | undefined;
     _get_next_segment_position(): string | undefined;
     _get_seq(): string;
     qualRaw(): Buffer | undefined;
@@ -28,6 +27,6 @@ export default class BamSlightlyLazyFeature implements Feature {
     children(): undefined;
     pairedFeature(): boolean;
     toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): import("./MismatchParser").Mismatch[];
+    _get_mismatches(): import("../MismatchParser").Mismatch[];
     _get_clipPos(): number;
 }

package/dist/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 // locals
-const MismatchParser_1 = require("./MismatchParser");
+const MismatchParser_1 = require("../MismatchParser");
 class BamSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class
     // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
@@ -28,20 +28,17 @@ class BamSlightlyLazyFeature {
     _get_pair_orientation() {
         return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
     }
-    _get_next_seq_id() {
-        return this.record._next_refid();
-    }
-    _get_seq_id() {
-        // @ts-ignore
-        return this.record._refID;
+    _get_next_ref() {
+        return this.record.isPaired()
+            ? this.adapter.refIdToName(this.record._next_refid())
+            : undefined;
     }
-    _get_next_refName() {
-        return this.adapter.refIdToName(this.record._next_refid());
+    _get_next_pos() {
+        return this.record.isPaired() ? this.record._next_pos() : undefined;
     }
     _get_next_segment_position() {
-        const { record, adapter } = this;
-        return record.isPaired()
-            ? `${adapter.refIdToName(record._next_refid())}:${record._next_pos() + 1}`
+        return this.record.isPaired()
+            ? `${this.adapter.refIdToName(this.record._next_refid())}:${this.record._next_pos() + 1}`
             : undefined;
     }
     _get_seq() {
@@ -57,9 +54,7 @@ class BamSlightlyLazyFeature {
             ...new Set(properties
                 .filter(prop => prop.startsWith('_get_') &&
                 prop !== '_get_mismatches' &&
-                prop !== '_get_tags' &&
-                prop !== '_get_next_seq_id' &&
-                prop !== '_get_seq_id')
+                prop !== '_get_tags')
                 .map(methodName => methodName.replace('_get_', ''))
                 .concat(this.record._tags())),
         ];
@@ -102,9 +97,7 @@ class BamSlightlyLazyFeature {
     }
     _get_clipPos() {
         const cigar = this.get('CIGAR') || '';
-        return this.get('strand') === -1
-            ? +(cigar.match(/(\d+)[SH]$/) || [])[1] || 0
-            : +(cigar.match(/^(\d+)([SH])/) || [])[1] || 0;
+        return (0, MismatchParser_1.getClip)(cigar, this.get('strand'));
     }
 }
 exports.default = BamSlightlyLazyFeature;

package/dist/BamAdapter/BamSlightlyLazyFeature.js.map

@@ -1 +1 @@
-{"version":3,"file":"BamSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/BamAdapter/BamSlightlyLazyFeature.ts"],"names":[],"mappings":";;AAOA,SAAS;AACT,qDAAgD;AAGhD,MAAqB,sBAAsB;IACzC,wEAAwE;IACxE,iFAAiF;IACjF,YACU,MAAiB,EACjB,OAAmB,EACnB,GAAY;QAFZ,WAAM,GAAN,MAAM,CAAW;QACjB,YAAO,GAAP,OAAO,CAAY;QACnB,QAAG,GAAH,GAAG,CAAS;IACnB,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,gBAAgB;QACd,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAA;IAClC,CAAC;IAED,WAAW;QACT,aAAa;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,MAAM,CAAA;IAC3B,CAAC;IAED,iBAAiB;QACf,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;IAC5D,CAAC;IAED,0BAA0B;QACxB,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;QAChC,OAAO,MAAM,CAAC,QAAQ,EAAE;YACtB,CAAC,CAAC,GAAG,OAAO,CAAC,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IAAI,MAAM,CAAC,SAAS,EAAE,GAAG,CAAC,EAAE;YAC1E,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAA;IAC9B,CAAC;IAED,GAAG,KAAI,CAAC;IAER,IAAI;QACF,MAAM,UAAU,GAAG,MAAM,CAAC,mBAAmB,CAC3C,sBAAsB,CAAC,SAAS,CACjC,CAAA;QAED,OAAO;YACL,GAAG,IAAI,GAAG,CACR,UAAU;iBACP,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;gBACxB,IAAI,KAAK,iBAAiB;gBAC1B,IAAI,KAAK,WAAW;gBACpB,IAAI,KAAK,kBAAkB;gBAC3B,IAAI,KAAK,aAAa,CACzB;iBACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;iBAClD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAC/B;SACF,CAAA;IACH,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,CAAA;IACjD,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC/B,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;IACvD,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,OAAO,IAAA,8BAAa,EAClB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EACjB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EACd,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EACf,IAAI,CAAC,GAAG,EACR,IAAI,CAAC,OAAO,EAAE,CACf,CAAA;IACH,CAAC;IAED,YAAY;QACV,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;QACrC,OAAO,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;YAC9B,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;YAC5C,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAClD,CAAC;CACF;AA/ID,yCA+IC"}
+{"version":3,"file":"BamSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/BamAdapter/BamSlightlyLazyFeature.ts"],"names":[],"mappings":";;AAOA,SAAS;AACT,sDAA0D;AAG1D,MAAqB,sBAAsB;IACzC,wEAAwE;IACxE,iFAAiF;IACjF,YACU,MAAiB,EACjB,OAAmB,EACnB,GAAY;QAFZ,WAAM,GAAN,MAAM,CAAW;QACjB,YAAO,GAAP,OAAO,CAAY;QACnB,QAAG,GAAH,GAAG,CAAS;IACnB,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;YACrD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IACrE,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IACpD,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,CAC5B,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAA;IAC9B,CAAC;IAED,GAAG,KAAI,CAAC;IAER,IAAI;QACF,MAAM,UAAU,GAAG,MAAM,CAAC,mBAAmB,CAC3C,sBAAsB,CAAC,SAAS,CACjC,CAAA;QAED,OAAO;YACL,GAAG,IAAI,GAAG,CACR,UAAU;iBACP,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;gBACxB,IAAI,KAAK,iBAAiB;gBAC1B,IAAI,KAAK,WAAW,CACvB;iBACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;iBAClD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAC/B;SACF,CAAA;IACH,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,CAAA;IACjD,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC/B,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;IACvD,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,OAAO,IAAA,8BAAa,EAClB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EACjB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EACd,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EACf,IAAI,CAAC,GAAG,EACR,IAAI,CAAC,OAAO,EAAE,CACf,CAAA;IACH,CAAC;IAED,YAAY;QACV,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;QACrC,OAAO,IAAA,wBAAO,EAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;IAC3C,CAAC;CACF;AAzID,yCAyIC"}

package/dist/BamAdapter/index.js

@@ -32,6 +32,7 @@ exports.default = (pluginManager) => {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'BamAdapter',
+            displayName: 'BAM adapter',
             configSchema: configSchema_1.default,
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BamAdapter'))).then(r => r.default),
         });

package/dist/BamAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BamAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,YAAY;YAClB,YAAY,EAAZ,sBAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,cAAc,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BamAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,YAAY;YAClB,WAAW,EAAE,aAAa;YAC1B,YAAY,EAAZ,sBAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,cAAc,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -1,7 +1,6 @@
 import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 import { CramRecord } from '@gmod/cram';
 import CramAdapter from './CramAdapter';
-import { Mismatch } from './util';
 export default class CramSlightlyLazyFeature implements Feature {
     private record;
     private _store;
@@ -17,25 +16,24 @@ export default class CramSlightlyLazyFeature implements Feature {
     _read_group_id(): string | undefined;
     _get_qual(): string;
     qualRaw(): number[] | null | undefined;
-    _get_seq_id(): string | undefined;
     _get_refName(): string | undefined;
     _get_is_paired(): boolean;
     _get_pair_orientation(): string | null | undefined;
     _get_template_length(): number | undefined;
-    _get_next_seq_id(): string | undefined;
-    _get_next_pos(): number | undefined;
+    _get_next_ref(): string | undefined;
     _get_next_segment_position(): string | undefined;
+    _get_next_pos(): number | undefined;
     _get_tags(): Record<string, string>;
     _get_seq(): string | null | undefined;
     _get_CIGAR(): string;
     tags(): string[];
     id(): string;
     get(field: string): any;
-    parent(): undefined | Feature;
-    children(): undefined | Feature[];
+    parent(): undefined;
+    children(): undefined;
     set(): void;
     pairedFeature(): boolean;
     _get_clipPos(): any;
     toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): Mismatch[];
+    _get_mismatches(): import("./util").Mismatch[];
 }

package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -43,11 +43,8 @@ class CramSlightlyLazyFeature {
     qualRaw() {
         return this.record.qualityScores;
     }
-    _get_seq_id() {
-        return this._store.refIdToName(this.record.sequenceId);
-    }
     _get_refName() {
-        return this._get_seq_id();
+        return this._store.refIdToName(this.record.sequenceId);
     }
     _get_is_paired() {
         return !!this.record.mate;
@@ -58,19 +55,20 @@ class CramSlightlyLazyFeature {
     _get_template_length() {
         return this.record.templateLength || this.record.templateSize;
     }
-    _get_next_seq_id() {
+    _get_next_ref() {
         return this.record.mate
             ? this._store.refIdToName(this.record.mate.sequenceId)
             : undefined;
     }
-    _get_next_pos() {
-        return this.record.mate ? this.record.mate.alignmentStart : undefined;
-    }
     _get_next_segment_position() {
         return this.record.mate
             ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${this.record.mate.alignmentStart}`
             : undefined;
     }
+    _get_next_pos() {
+        var _a;
+        return (_a = this.record.mate) === null || _a === void 0 ? void 0 : _a.alignmentStart;
+    }
     _get_tags() {
         const RG = this._read_group_id();
         const { tags } = this.record;

package/dist/CramAdapter/CramSlightlyLazyFeature.js.map

@@ -1 +1 @@
-{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":";;AAOA,iCAAgF;AAEhF,MAAqB,uBAAuB;IAC1C,wEAAwE;IACxE,iFAAiF;IACjF,YAAoB,MAAkB,EAAU,MAAmB;QAA/C,WAAM,GAAN,MAAM,CAAY;QAAU,WAAM,GAAN,MAAM,CAAa;IAAG,CAAC;IAEvE,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,CAAA;IACvC,CAAC;IAED,QAAQ;;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,MAAA,IAAI,CAAC,MAAM,CAAC,WAAW,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACxE,CAAC;IAED,uBAAuB;QACrB,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IACjC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,CAAA;IACnC,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,cAAc;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAA;QAC3C,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACrD,CAAC;IAED,SAAS;QACP,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACpD,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,aAAa,CAAA;IAClC,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACxD,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,WAAW,EAAE,CAAA;IAC3B,CAAC;IAED,cAAc;QACZ,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAA;IAC3B,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,oBAAoB;QAClB,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,IAAI,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IAC/D,CAAC;IAED,gBAAgB;QACd,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC;YACtD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,SAAS,CAAA;IACvE,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,IACrD,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cACnB,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,SAAS;QACP,MAAM,EAAE,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAA;QAC5B,4DAA4D;QAC5D,OAAO,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;IAClD,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,kDAAkD;IAClD,UAAU;QACR,OAAO,IAAA,0BAAmB,EACxB,IAAI,CAAC,MAAM,CAAC,YAAY,EACxB,IAAI,CAAC,MAAM,CAAC,cAAc,EAC1B,IAAI,CAAC,MAAM,CAAC,UAAU,EACtB,IAAI,CAAC,MAAM,CAAC,UAAU,CACvB,CAAA;IACH,CAAC;IAED,IAAI;QACF,OAAO,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,CAAC,SAAS,CAAC;aACjE,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;YACxB,IAAI,KAAK,iBAAiB;YAC1B,IAAI,KAAK,yBAAyB,CACrC;aACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;IACpD,CAAC;IAED,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,GAAG,KAAU,CAAC;IAEd,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,YAAY;QACV,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;QACzC,IAAI,UAAU,CAAC,MAAM,EAAE;YACrB,MAAM,MAAM,GACV,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;gBACvB,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC;gBACnC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;YAChC,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,EAAE;gBAC9C,OAAO,OAAO,CAAA;aACf;SACF;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;QAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,EAAE,CAAA;QAC3B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAC/B,OAAO,IAAA,+BAAwB,EAAC,YAAY,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IAC5D,CAAC;CACF;AApLD,0CAoLC"}
+{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":";;AASA,iCAAsE;AAEtE,MAAqB,uBAAuB;IAC1C,wEAAwE;IACxE,iFAAiF;IACjF,YAAoB,MAAkB,EAAU,MAAmB;QAA/C,WAAM,GAAN,MAAM,CAAY;QAAU,WAAM,GAAN,MAAM,CAAa;IAAG,CAAC;IAEvE,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,CAAA;IACvC,CAAC;IAED,QAAQ;;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,MAAA,IAAI,CAAC,MAAM,CAAC,WAAW,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACxE,CAAC;IAED,uBAAuB;QACrB,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IACjC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,CAAA;IACnC,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,cAAc;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAA;QAC3C,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACrD,CAAC;IAED,SAAS;QACP,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACpD,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,aAAa,CAAA;IAClC,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACxD,CAAC;IAED,cAAc;QACZ,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAA;IAC3B,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,oBAAoB;QAClB,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,IAAI,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IAC/D,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC;YACtD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,IACrD,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cACnB,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;;QACX,OAAO,MAAA,IAAI,CAAC,MAAM,CAAC,IAAI,0CAAE,cAAc,CAAA;IACzC,CAAC;IAED,SAAS;QACP,MAAM,EAAE,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAA;QAC5B,4DAA4D;QAC5D,OAAO,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;IAClD,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,kDAAkD;IAClD,UAAU;QACR,OAAO,IAAA,0BAAmB,EACxB,IAAI,CAAC,MAAM,CAAC,YAAY,EACxB,IAAI,CAAC,MAAM,CAAC,cAAc,EAC1B,IAAI,CAAC,MAAM,CAAC,UAAU,EACtB,IAAI,CAAC,MAAM,CAAC,UAAU,CACvB,CAAA;IACH,CAAC;IAED,IAAI;QACF,OAAO,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,CAAC,SAAS,CAAC;aACjE,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;YACxB,IAAI,KAAK,iBAAiB;YAC1B,IAAI,KAAK,yBAAyB,CACrC;aACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;IACpD,CAAC;IAED,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,GAAG,KAAI,CAAC;IAER,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,YAAY;QACV,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;QACzC,IAAI,UAAU,CAAC,MAAM,EAAE;YACrB,MAAM,MAAM,GACV,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;gBACvB,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC;gBACnC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;YAChC,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,EAAE;gBAC9C,OAAO,OAAO,CAAA;aACf;SACF;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;QAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,EAAE,CAAA;QAC3B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAC/B,OAAO,IAAA,+BAAwB,EAAC,YAAY,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IAC5D,CAAC;CACF;AAhLD,0CAgLC"}

package/dist/CramAdapter/index.js

@@ -33,6 +33,7 @@ exports.default = (pluginManager) => {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'CramAdapter',
+            displayName: 'CRAM adapter',
             configSchema: configSchema_1.default,
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
         });

package/dist/CramAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,SAAS;AACT,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,aAAa;YACnB,YAAY,EAAZ,sBAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,eAAe,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACpE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,SAAS;AACT,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,aAAa;YACnB,WAAW,EAAE,cAAc;YAC3B,YAAY,EAAZ,sBAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,eAAe,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACpE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/GuessAlignmentsTypes/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/GuessAlignmentsTypes/index.js

@@ -0,0 +1,56 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const tracks_1 = require("@jbrowse/core/util/tracks");
+exports.default = (pluginManager) => {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.cram$/i;
+            const adapterName = 'CramAdapter';
+            const fileName = (0, tracks_1.getFileName)(file);
+            const obj = {
+                type: adapterName,
+                cramLocation: file,
+                craiLocation: index || (0, tracks_1.makeIndex)(file, '.crai'),
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.bam$/i;
+            const adapterName = 'BamAdapter';
+            const fileName = (0, tracks_1.getFileName)(file);
+            const indexName = index && (0, tracks_1.getFileName)(index);
+            const obj = {
+                type: adapterName,
+                bamLocation: file,
+                index: {
+                    location: index || (0, tracks_1.makeIndex)(file, '.bai'),
+                    indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'BAI'),
+                },
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => {
+            if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
+                return 'AlignmentsTrack';
+            }
+            return trackTypeGuesser(adapterName);
+        };
+    });
+};
+//# sourceMappingURL=index.js.map

package/dist/GuessAlignmentsTypes/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GuessAlignmentsTypes/index.ts"],"names":[],"mappings":";;AAEA,sDAMkC;AAElC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,UAAU,GAAG,UAAU,CAAA;YAC7B,MAAM,WAAW,GAAG,aAAa,CAAA;YACjC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;YAClC,MAAM,GAAG,GAAG;gBACV,IAAI,EAAE,WAAW;gBACjB,YAAY,EAAE,IAAI;gBAClB,YAAY,EAAE,KAAK,IAAI,IAAA,kBAAS,EAAC,IAAI,EAAE,OAAO,CAAC;aAChD,CAAA;YACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;gBAC7C,OAAO,GAAG,CAAA;aACX;iBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;gBACtC,OAAO,GAAG,CAAA;aACX;YACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;QACjD,CAAC,CAAA;IACH,CAAC,CACF,CAAA;IAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,UAAU,GAAG,SAAS,CAAA;YAC5B,MAAM,WAAW,GAAG,YAAY,CAAA;YAChC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;YAClC,MAAM,SAAS,GAAG,KAAK,IAAI,IAAA,oBAAW,EAAC,KAAK,CAAC,CAAA;YAE7C,MAAM,GAAG,GAAG;gBACV,IAAI,EAAE,WAAW;gBACjB,WAAW,EAAE,IAAI;gBACjB,KAAK,EAAE;oBACL,QAAQ,EAAE,KAAK,IAAI,IAAA,kBAAS,EAAC,IAAI,EAAE,MAAM,CAAC;oBAC1C,SAAS,EAAE,IAAA,sBAAa,EAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;iBAClD;aACF,CAAA;YACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;gBAC7C,OAAO,GAAG,CAAA;aACX;iBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;gBACtC,OAAO,GAAG,CAAA;aACX;YACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;QACjD,CAAC,CAAA;IACH,CAAC,CACF,CAAA;IACD,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;QACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;YAC7B,IAAI,WAAW,KAAK,YAAY,IAAI,WAAW,KAAK,aAAa,EAAE;gBACjE,OAAO,iBAAiB,CAAA;aACzB;YACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;QACtC,CAAC,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC,CAAA"}

package/dist/HtsgetBamAdapter/index.js

@@ -29,16 +29,16 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const configSchema_1 = __importDefault(require("./configSchema"));
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 exports.default = (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'HtsgetBamAdapter',
-        adapterMetadata: {
-            category: null,
-            hiddenFromGUI: true,
-            displayName: null,
-            description: null,
-        },
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./HtsgetBamAdapter'))).then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType_1.default({
+            name: 'HtsgetBamAdapter',
+            displayName: 'Htsget BAM adapter',
+            adapterMetadata: {
+                hiddenFromGUI: true,
+            },
+            configSchema: configSchema_1.default,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./HtsgetBamAdapter'))).then(r => r.default),
+        });
+    });
 };
 //# sourceMappingURL=index.js.map

package/dist/HtsgetBamAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kEAAyC;AAEzC,kGAAyE;AAEzE,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,kBAAkB;QACxB,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;YACjB,WAAW,EAAE,IAAI;SAClB;QACD,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,oBAAoB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kEAAyC;AAEzC,kGAAyE;AAEzE,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,kBAAkB;YACxB,WAAW,EAAE,oBAAoB;YACjC,eAAe,EAAE;gBACf,aAAa,EAAE,IAAI;aACpB;YACD,YAAY,EAAZ,sBAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,oBAAoB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACzE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -16,24 +16,21 @@ const useStyles = (0, mui_1.makeStyles)()(() => ({
     },
 }));
 function AlignmentsDisplay({ model }) {
-    const { PileupDisplay, SNPCoverageDisplay, showPileup, showCoverage } = model;
+    const { PileupDisplay, SNPCoverageDisplay } = model;
     const { classes } = useStyles();
     const top = SNPCoverageDisplay.height;
     return (react_1.default.createElement("div", { "data-testid": `display-${(0, configuration_1.getConf)(model, 'displayId')}`, style: { position: 'relative' } },
-        showCoverage ? (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement("div", { "data-testid": "Blockset-snpcoverage" },
-                react_1.default.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
-            react_1.default.createElement(ui_1.ResizeHandle, { onDrag: delta => {
-                    SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
-                    return delta;
-                }, className: classes.resizeHandle, style: {
-                    top,
-                } }))) : null,
-        showPileup ? (react_1.default.createElement("div", { "data-testid": "Blockset-pileup", style: {
+        react_1.default.createElement("div", { "data-testid": "Blockset-snpcoverage" },
+            react_1.default.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
+        react_1.default.createElement(ui_1.ResizeHandle, { onDrag: delta => {
+                SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
+                return delta;
+            }, className: classes.resizeHandle, style: { top } }),
+        react_1.default.createElement("div", { "data-testid": "Blockset-pileup", style: {
                 position: 'absolute',
-                top: showCoverage ? SNPCoverageDisplay.height : 0,
+                top,
             } },
-            react_1.default.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))) : null));
+            react_1.default.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))));
 }
 exports.default = (0, mobx_react_1.observer)(AlignmentsDisplay);
 //# sourceMappingURL=AlignmentsDisplay.js.map

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map

@@ -1 +1 @@
-{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,uCAA0C;AAC1C,+DAAqD;AACrD,yCAA+C;AAK/C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,GAAG,EAAE,CAAC,CAAC;IACpC,YAAY,EAAE;QACZ,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAAqC;IACrE,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,UAAU,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IAC7E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,kBAAkB,CAAC,MAAM,CAAA;IACrC,OAAO,CACL,sDACe,WAAW,IAAA,uBAAO,EAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE9B,YAAY,CAAC,CAAC,CAAC,CACd;YACE,sDAAiB,sBAAsB;gBACrC,8BAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;YACN,8BAAC,iBAAY,IACX,MAAM,EAAE,KAAK,CAAC,EAAE;oBACd,kBAAkB,CAAC,SAAS,CAAC,kBAAkB,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;oBAC/D,OAAO,KAAK,CAAA;gBACd,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE;oBACL,GAAG;iBACJ,GACD,CACD,CACJ,CAAC,CAAC,CAAC,IAAI;QAEP,UAAU,CAAC,CAAC,CAAC,CACZ,sDACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,YAAY,CAAC,CAAC,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;aAClD;YAED,8BAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,iBAAiB,CAAC,CAAA"}
+{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,uCAA0C;AAC1C,+DAAqD;AACrD,yCAA+C;AAK/C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,GAAG,EAAE,CAAC,CAAC;IACpC,YAAY,EAAE;QACZ,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAAqC;IACrE,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,kBAAkB,CAAC,MAAM,CAAA;IACrC,OAAO,CACL,sDACe,WAAW,IAAA,uBAAO,EAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE/B,sDAAiB,sBAAsB;YACrC,8BAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;QACN,8BAAC,iBAAY,IACX,MAAM,EAAE,KAAK,CAAC,EAAE;gBACd,kBAAkB,CAAC,SAAS,CAAC,kBAAkB,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;gBAC/D,OAAO,KAAK,CAAA;YACd,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE,EAAE,GAAG,EAAE,GACd;QAEF,sDACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG;aACJ;YAED,8BAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACF,CACP,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,iBAAiB,CAAC,CAAA"}

package/dist/LinearAlignmentsDisplay/index.js

@@ -13,6 +13,7 @@ function default_1(pluginManager) {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
             name: 'LinearAlignmentsDisplay',
+            displayName: 'Alignments display (combination)',
             configSchema,
             stateModel: (0, model_1.default)(pluginManager, configSchema),
             trackType: 'AlignmentsTrack',

package/dist/LinearAlignmentsDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearAlignmentsDisplay/index.ts"],"names":[],"mappings":";;;;;AAAA,kGAAyE;AAEzE,SAAS;AACT,yEAAuD;AACvD,2DAAyC;AACzC,uFAA2D;AAE3D,mBAAyB,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,yBAAyB;YAC/B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAd,2BAAc;SACf,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAZD,4BAYC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearAlignmentsDisplay/index.ts"],"names":[],"mappings":";;;;;AAAA,kGAAyE;AAEzE,SAAS;AACT,yEAAuD;AACvD,2DAAyC;AACzC,uFAA2D;AAE3D,mBAAyB,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,yBAAyB;YAC/B,WAAW,EAAE,kCAAkC;YAC/C,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAd,2BAAc;SACf,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAbD,4BAaC"}

package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts

@@ -1,4 +1,7 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configModelFactory: (pm: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export type AlignmentsConfigModel = ReturnType<typeof configModelFactory>;
-export default configModelFactory;
+/**
+ * #config LinearAlignmentsDisplay
+ * has a "pileup" sub-display, where you can see individual reads and a
+ * quantitative "snpcoverage" sub-display track showing SNP frequencies
+ */
+export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/LinearAlignmentsDisplay/models/configSchema.js

@@ -7,8 +7,7 @@ const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view"
  * has a "pileup" sub-display, where you can see individual reads and a
  * quantitative "snpcoverage" sub-display track showing SNP frequencies
  */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const configModelFactory = (pm) => {
+function configModelFactory(pm) {
     return (0, configuration_1.ConfigurationSchema)('LinearAlignmentsDisplay', {
         /**
          * #slot
@@ -26,6 +25,6 @@ const configModelFactory = (pm) => {
         baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });
-};
+}
 exports.default = configModelFactory;
 //# sourceMappingURL=configSchema.js.map

package/dist/LinearAlignmentsDisplay/models/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAAkF;AAGlF;;;;GAIG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,kBAAkB,GAAG,CAAC,EAAiB,EAAE,EAAE;IAC/C,OAAO,IAAA,mCAAmB,EACxB,yBAAyB,EACzB;QACE;;WAEG;QACH,aAAa,EAAE,EAAE,CAAC,cAAc,CAAC,qBAAqB,CAAC,CAAC,YAAY;QACpE;;WAEG;QACH,kBAAkB,EAAE,EAAE,CAAC,cAAc,CAAC,0BAA0B,CAAC;aAC9D,YAAY;KAChB,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,yDAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC,CAAA;AAGD,kBAAe,kBAAkB,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAAkF;AAGlF;;;;GAIG;AACH,SAAwB,kBAAkB,CAAC,EAAiB;IAC1D,OAAO,IAAA,mCAAmB,EACxB,yBAAyB,EACzB;QACE;;WAEG;QACH,aAAa,EAAE,EAAE,CAAC,cAAc,CAAC,qBAAqB,CAAC,CAAC,YAAY;QAEpE;;WAEG;QACH,kBAAkB,EAAE,EAAE,CAAC,cAAc,CAAC,0BAA0B,CAAC;aAC9D,YAAY;KAChB,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,yDAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAvBD,qCAuBC"}

package/dist/LinearAlignmentsDisplay/models/model.d.ts

@@ -1,8 +1,8 @@
 import React from 'react';
+import { Instance, IStateTreeNode } from 'mobx-state-tree';
 import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { MenuItem } from '@jbrowse/core/ui';
-import { Instance } from 'mobx-state-tree';
 /**
  * #stateModel LinearAlignmentsDisplay
  * extends `BaseDisplay`
@@ -12,15 +12,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
-    PileupDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
+    PileupDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
     SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
     snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
     type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
     height: import("mobx-state-tree").IType<number | undefined, number, number>;
-    showCoverage: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    showPileup: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -33,11 +32,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+        } & IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>; /**
-             * #property
-             */
+            type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
@@ -54,16 +51,16 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
-             * #action
-             */
+        } & IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
+         * #property
+         */
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
@@ -80,14 +77,6 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     scrollTop: number;
 } & {
-    /**
-     * #action
-     */
-    toggleCoverage(): void;
-    /**
-     * #action
-     */
-    togglePileup(): void;
     /**
      * #action
      */
@@ -100,7 +89,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #getter
      */
-    readonly pileupDisplayConfig: any;
+    readonly pileupConf: any;
     /**
      * #method
      */
@@ -124,19 +113,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #getter
      */
-    readonly sortedByPosition: any;
-    /**
-     * #getter
-     */
-    readonly sortedByRefName: any;
-    /**
-     * #getter
-     */
-    readonly snpCoverageDisplayConfig: any;
-    /**
-     * #method
-     */
-    trackMenuItems(): MenuItem[];
+    readonly coverageConf: any;
 } & {
     /**
      * #action
@@ -153,7 +130,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #action
      */
-    setHeight(displayHeight: number): number;
+    setHeight(n: number): number;
+    /**
+     * #action
+     */
+    setLowerPanelType(type: string): void;
     /**
      * #action
      */
@@ -166,6 +147,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<JSX.Element>;
+} & {
+    /**
+     * #method
+     */
+    trackMenuItems(): MenuItem[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;
 export type AlignmentsDisplayStateModel = ReturnType<typeof stateModelFactory>;