@jbrowse/plugin-alignments 2.0.0 → 2.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/BamAdapter/MismatchParser.d.ts +1 -1
- package/dist/BamAdapter/MismatchParser.js +2 -1
- package/dist/BamAdapter/MismatchParser.js.map +1 -1
- package/esm/BamAdapter/MismatchParser.d.ts +1 -1
- package/esm/BamAdapter/MismatchParser.js +2 -2
- package/esm/BamAdapter/MismatchParser.js.map +1 -1
- package/package.json +5 -5
- package/src/BamAdapter/MismatchParser.ts +2 -2
|
@@ -9,7 +9,7 @@ export interface Mismatch {
|
|
|
9
9
|
seq?: string;
|
|
10
10
|
cliplen?: number;
|
|
11
11
|
}
|
|
12
|
-
export declare function parseCigar(cigar
|
|
12
|
+
export declare function parseCigar(cigar?: string): string[];
|
|
13
13
|
export declare function cigarToMismatches(ops: string[], seq: string, ref?: string, qual?: Buffer): Mismatch[];
|
|
14
14
|
/**
|
|
15
15
|
* parse a SAM MD tag to find mismatching bases of the template versus the reference
|
|
@@ -48,7 +48,8 @@ var util_1 = require("@jbrowse/core/util");
|
|
|
48
48
|
var mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
|
|
49
49
|
var modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
|
|
50
50
|
function parseCigar(cigar) {
|
|
51
|
-
|
|
51
|
+
if (cigar === void 0) { cigar = ''; }
|
|
52
|
+
return cigar.split(/([MIDNSHPX=])/).slice(0, -1);
|
|
52
53
|
}
|
|
53
54
|
exports.parseCigar = parseCigar;
|
|
54
55
|
function cigarToMismatches(ops, seq, ref, qual) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"MismatchParser.js","sourceRoot":"","sources":["../../src/BamAdapter/MismatchParser.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2CAA2C;AAW3C,IAAM,OAAO,GAAG,IAAI,MAAM,CAAC,wBAAwB,CAAC,CAAA;AACpD,IAAM,iBAAiB,GAAG,IAAI,MAAM,CAAC,+BAA+B,CAAC,CAAA;AACrE,SAAgB,UAAU,CAAC,
|
|
1
|
+
{"version":3,"file":"MismatchParser.js","sourceRoot":"","sources":["../../src/BamAdapter/MismatchParser.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2CAA2C;AAW3C,IAAM,OAAO,GAAG,IAAI,MAAM,CAAC,wBAAwB,CAAC,CAAA;AACpD,IAAM,iBAAiB,GAAG,IAAI,MAAM,CAAC,+BAA+B,CAAC,CAAA;AACrE,SAAgB,UAAU,CAAC,KAAU;IAAV,sBAAA,EAAA,UAAU;IACnC,OAAO,KAAK,CAAC,KAAK,CAAC,eAAe,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;AAClD,CAAC;AAFD,gCAEC;AACD,SAAgB,iBAAiB,CAC/B,GAAa,EACb,GAAW,EACX,GAAY,EACZ,IAAa;IAEb,IAAI,OAAO,GAAG,CAAC,CAAA,CAAC,mBAAmB;IACnC,IAAI,OAAO,GAAG,CAAC,CAAA,CAAC,aAAa;IAC7B,IAAM,UAAU,GAAe,EAAE,CAAA;IACjC,IAAM,YAAY,GAAG,GAAG,IAAI,GAAG,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QACtC,IAAM,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;QACnB,IAAM,EAAE,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;QAErB,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;YAC1C,IAAI,YAAY,EAAE;gBAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE;oBAC5B;oBACE,sHAAsH;oBACtH,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,KAAK,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,EACjE;wBACA,UAAU,CAAC,IAAI,CAAC;4BACd,KAAK,EAAE,OAAO,GAAG,CAAC;4BAClB,IAAI,EAAE,UAAU;4BAChB,IAAI,EAAE,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC;4BACtB,OAAO,EAAE,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC;4BACzB,MAAM,EAAE,CAAC;yBACV,CAAC,CAAA;qBACH;iBACF;aACF;YACD,OAAO,IAAI,GAAG,CAAA;SACf;QACD,IAAI,EAAE,KAAK,GAAG,EAAE;YACd,UAAU,CAAC,IAAI,CAAC;gBACd,KAAK,EAAE,OAAO;gBACd,IAAI,EAAE,WAAW;gBACjB,IAAI,EAAE,UAAG,GAAG,CAAE;gBACd,MAAM,EAAE,CAAC;aACV,CAAC,CAAA;YACF,OAAO,IAAI,GAAG,CAAA;SACf;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,UAAU,CAAC,IAAI,CAAC;gBACd,KAAK,EAAE,OAAO;gBACd,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,GAAG;gBACT,MAAM,EAAE,GAAG;aACZ,CAAC,CAAA;SACH;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,UAAU,CAAC,IAAI,CAAC;gBACd,KAAK,EAAE,OAAO;gBACd,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,GAAG;gBACT,MAAM,EAAE,GAAG;aACZ,CAAC,CAAA;SACH;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,IAAM,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC,OAAO,EAAE,OAAO,GAAG,GAAG,CAAC,CAAA;YAC3C,IAAM,CAAC,GAAG,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,KAAK,CAAC,OAAO,EAAE,OAAO,GAAG,GAAG,CAAC,KAAI,EAAE,CAAA;YAEnD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE;gBAC5B,UAAU,CAAC,IAAI,CAAC;oBACd,KAAK,EAAE,OAAO,GAAG,CAAC;oBAClB,IAAI,EAAE,UAAU;oBAChB,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;oBACV,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;oBACV,MAAM,EAAE,CAAC;iBACV,CAAC,CAAA;aACH;YACD,OAAO,IAAI,GAAG,CAAA;SACf;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,UAAU,CAAC,IAAI,CAAC;gBACd,KAAK,EAAE,OAAO;gBACd,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,WAAI,GAAG,CAAE;gBACf,OAAO,EAAE,GAAG;gBACZ,MAAM,EAAE,CAAC;aACV,CAAC,CAAA;SACH;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,UAAU,CAAC,IAAI,CAAC;gBACd,KAAK,EAAE,OAAO;gBACd,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,WAAI,GAAG,CAAE;gBACf,OAAO,EAAE,GAAG;gBACZ,MAAM,EAAE,CAAC;aACV,CAAC,CAAA;YACF,OAAO,IAAI,GAAG,CAAA;SACf;QAED,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;YAC1C,OAAO,IAAI,GAAG,CAAA;SACf;KACF;IACD,OAAO,UAAU,CAAA;AACnB,CAAC;AA7FD,8CA6FC;AAED;;;GAGG;AACH,SAAgB,cAAc,CAC5B,QAAgB,EAChB,GAAa,EACb,eAA2B,EAC3B,GAAW,EACX,IAAa;IAEb,IAAM,eAAe,GAAe,EAAE,CAAA;IACtC,IAAI,IAAI,GAAa,EAAE,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,IAAI,EAAE,UAAU,EAAE,CAAA;IACxE,IAAM,KAAK,GAAG,eAAe,CAAC,MAAM,CAAC,UAAA,KAAK,IAAI,OAAA,KAAK,CAAC,IAAI,KAAK,MAAM,EAArB,CAAqB,CAAC,CAAA;IACpE,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,kBAAkB,GAAG,CAAC,CAAA;IAC1B,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,IAAI,WAAW,GAAG,CAAC,CAAA;IAEnB,6DAA6D;IAC7D,8DAA8D;IAC9D,oBAAoB;IAEpB,SAAS,UAAU;QACjB,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAE1B,kCAAkC;QAClC,IAAI,GAAG;YACL,KAAK,EAAE,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,MAAM;YAC/B,MAAM,EAAE,CAAC;YACT,IAAI,EAAE,EAAE;YACR,IAAI,EAAE,UAAU;SACjB,CAAA;IACH,CAAC;IAED,SAAS,qBAAqB,CAAC,QAAgB;QAC7C,IAAI,cAAc,GAAG,kBAAkB,CAAA;QACvC,IAAI,SAAS,GAAG,aAAa,CAAA;QAC7B,KACE,IAAI,CAAC,GAAG,SAAS,EACjB,CAAC,GAAG,GAAG,CAAC,MAAM,IAAI,SAAS,IAAI,QAAQ,EACvC,CAAC,IAAI,CAAC,EAAE,SAAS,GAAG,CAAC,EACrB;YACA,IAAM,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACnB,IAAM,EAAE,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;YAErB,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;gBAC5B,cAAc,IAAI,GAAG,CAAA;aACtB;iBAAM,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;gBACjD,SAAS,IAAI,GAAG,CAAA;aACjB;iBAAM,IAAI,EAAE,KAAK,GAAG,EAAE;gBACrB,cAAc,IAAI,GAAG,CAAA;gBACrB,SAAS,IAAI,GAAG,CAAA;aACjB;SACF;QACD,kBAAkB,GAAG,cAAc,CAAA;QACnC,aAAa,GAAG,SAAS,CAAA;QAEzB,OAAO,cAAc,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAC,CAAA;IAChD,CAAC;IAED,mCAAmC;IACnC,IAAM,EAAE,GAAG,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;IACxC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAClC,IAAM,KAAK,GAAG,EAAE,CAAC,CAAC,CAAC,CAAA;QACnB,IAAM,GAAG,GAAG,CAAC,KAAK,CAAA;QAClB,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE;YACtB,IAAI,CAAC,KAAK,IAAI,GAAG,CAAA;SAClB;aAAM,IAAI,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YAChC,IAAI,CAAC,KAAK,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,CAAA;SAC/B;aAAM;YACL,WAAW;YACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;gBACxC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAA;gBAEf,OAAO,WAAW,GAAG,KAAK,CAAC,MAAM,EAAE;oBACjC,IAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAA;oBACnC,IAAI,IAAI,CAAC,KAAK,IAAI,QAAQ,CAAC,KAAK,EAAE;wBAChC,IAAI,CAAC,KAAK,IAAI,QAAQ,CAAC,MAAM,CAAA;wBAC7B,WAAW,EAAE,CAAA;qBACd;yBAAM;wBACL,MAAK;qBACN;iBACF;gBACD,IAAM,CAAC,GAAG,qBAAqB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBAC3C,IAAI,CAAC,IAAI,GAAG,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG,CAAA;gBACzB,IAAM,SAAS,GAAG,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAG,CAAC,CAAC,CAAA;gBAC3B,IAAI,SAAS,EAAE;oBACb,IAAI,CAAC,IAAI,GAAG,SAAS,CAAA;iBACtB;gBACD,IAAI,CAAC,OAAO,GAAG,KAAK,CAAA;gBACpB,UAAU,EAAE,CAAA;aACb;SACF;KACF;IACD,OAAO,eAAe,CAAA;AACxB,CAAC;AA5FD,wCA4FC;AAED,SAAgB,aAAa,CAC3B,KAAa,EACb,EAAU,EACV,GAAW,EACX,GAAY,EACZ,IAAa;IAEb,IAAI,UAAU,GAAe,EAAE,CAAA;IAC/B,IAAM,GAAG,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAE7B,oCAAoC;IACpC,IAAI,KAAK,EAAE;QACT,UAAU,GAAG,UAAU,CAAC,MAAM,CAAC,iBAAiB,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,IAAI,CAAC,CAAC,CAAA;KACvE;IAED,2CAA2C;IAC3C,IAAI,EAAE,EAAE;QACN,UAAU,GAAG,UAAU,CAAC,MAAM,CAC5B,cAAc,CAAC,EAAE,EAAE,GAAG,EAAE,UAAU,EAAE,GAAG,EAAE,IAAI,CAAC,CAC/C,CAAA;KACF;IAED,OAAO,UAAU,CAAA;AACnB,CAAC;AAvBD,sCAuBC;AACD,4EAA4E;AAC5E,oBAAoB;AACpB,SAAiB,aAAa,CAAC,QAAkB,EAAE,SAAmB;;;;;gBAChE,OAAO,GAAG,CAAC,CAAA;gBACX,MAAM,GAAG,CAAC,CAAA;gBACV,OAAO,GAAG,CAAC,CAAA;gBAEN,CAAC,GAAG,CAAC;;;qBAAE,CAAA,CAAC,GAAG,QAAQ,CAAC,MAAM,IAAI,OAAO,GAAG,SAAS,CAAC,MAAM,CAAA;gBACzD,GAAG,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;gBAClB,EAAE,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;qBACtB,CAAA,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,CAAA,EAAxB,wBAAwB;gBAC1B,KAAS,MAAI,CAAC,EAAE,GAAC,GAAG,GAAG,IAAI,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,GAAC,EAAE,EAAE;oBAC1D,IAAI,SAAS,CAAC,OAAO,CAAC,KAAK,OAAO,GAAG,GAAC,EAAE;wBACtC,OAAO,EAAE,CAAA;qBACV;iBACF;gBACD,OAAO,IAAI,GAAG,CAAA;;;qBACL,CAAA,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,CAAA,EAAxB,wBAAwB;gBACjC,MAAM,IAAI,GAAG,CAAA;;;qBACJ,CAAA,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,CAAA,EAAtC,wBAAsC;gBACtC,MAAI,CAAC;;;qBAAE,CAAA,GAAC,GAAG,GAAG,IAAI,OAAO,GAAG,SAAS,CAAC,MAAM,CAAA;qBAC/C,CAAA,SAAS,CAAC,OAAO,CAAC,KAAK,OAAO,GAAG,GAAC,CAAA,EAAlC,wBAAkC;gBACpC,qBAAM,MAAM,GAAG,GAAC,EAAA;;gBAAhB,SAAgB,CAAA;gBAChB,OAAO,EAAE,CAAA;;;gBAH0C,GAAC,EAAE,CAAA;;;gBAM1D,OAAO,IAAI,GAAG,CAAA;gBACd,MAAM,IAAI,GAAG,CAAA;;;gBApBkD,CAAC,IAAI,CAAC,CAAA;;;;;CAuB1E;AA5BD,sCA4BC;AACD,SAAgB,wBAAwB,CACtC,EAAU,EACV,IAAY,EACZ,OAAe;IAEf,IAAM,GAAG,GAAG,OAAO,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAA,aAAM,EAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;IAChD,IAAM,IAAI,GAAG,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,UAAA,GAAG,IAAI,OAAA,CAAC,CAAC,GAAG,EAAL,CAAK,CAAC,CAAA;IAC/C,IAAM,MAAM,GAAG,EAAE,CAAA;IACjB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACpC,IAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACb,IAAA,KAAA,OAAsB,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA,EAAnC,OAAO,QAAA,EAAK,KAAK,cAAkB,CAAA;QAE1C,8CAA8C;QAC9C,IAAM,OAAO,GAAG,OAAO,CAAC,KAAK,CAAC,iBAAiB,CAAC,CAAA;QAChD,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAA;SACzC;QACK,IAAA,KAAA,OAA4B,OAAO,IAAA,EAAhC,IAAI,QAAA,EAAE,MAAM,QAAA,EAAE,OAAO,QAAW,CAAA;QAEzC,oEAAoE;QACpE,kEAAkE;QAClE,IAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,EAAH,CAAG,CAAC,CAAA;QAEvD,IAAI,MAAM,KAAK,GAAG,EAAE;YAClB,OAAO,CAAC,IAAI,CAAC,2CAA2C,CAAC,CAAA;YACzD,iEAAiE;YACjE,MAAM,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,SAAS,EAAE,EAAc,EAAE,CAAC,CAAA;SAChE;QAED,qEAAqE;QACrE,wEAAwE;QACxE,wEAAwE;QACxE,IAAI;QACJ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACrC,IAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACrB,IAAI,GAAC,GAAG,CAAC,CAAA;YACT,IAAM,SAAS,GAAG,EAAE,CAAA;YACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACrC,IAAI,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBACrB,GAAG;oBACD,IAAI,IAAI,KAAK,GAAG,IAAI,IAAI,KAAK,GAAG,CAAC,GAAC,CAAC,EAAE;wBACnC,KAAK,EAAE,CAAA;qBACR;oBACD,GAAC,EAAE,CAAA;iBACJ,QAAQ,KAAK,IAAI,CAAC,IAAI,GAAC,GAAG,GAAG,CAAC,MAAM,EAAC;gBAEtC,IAAM,IAAI,GAAG,GAAC,GAAG,CAAC,CAAA;gBAClB,SAAS,CAAC,IAAI,CAAC,OAAO,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;aAC9D;YACD,IAAI,OAAO,KAAK,CAAC,CAAC,EAAE;gBAClB,SAAS,CAAC,IAAI,CAAC,UAAC,CAAC,EAAE,CAAC,IAAK,OAAA,CAAC,GAAG,CAAC,EAAL,CAAK,CAAC,CAAA;aAChC;YACD,MAAM,CAAC,IAAI,CAAC;gBACV,IAAI,MAAA;gBACJ,SAAS,WAAA;aACV,CAAC,CAAA;SACH;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AA3DD,4DA2DC;AAED,SAAgB,oBAAoB,CAAC,EAAU;IAC7C,IAAM,IAAI,GAAG,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IAC1B,OAAO,IAAI;SACR,MAAM,CAAC,UAAA,GAAG,IAAI,OAAA,CAAC,CAAC,GAAG,EAAL,CAAK,CAAC;SACpB,GAAG,CAAC,UAAA,GAAG;QACA,IAAA,KAAA,OAAY,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,IAAA,EAAzB,OAAO,QAAkB,CAAA;QAEhC,IAAM,OAAO,GAAG,OAAO,CAAC,KAAK,CAAC,iBAAiB,CAAC,CAAA;QAChD,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAA;SACzC;QACK,IAAA,KAAA,OAAkB,OAAO,IAAA,EAAlB,OAAO,QAAW,CAAA;QAE/B,oEAAoE;QACpE,kEAAkE;QAClE,OAAO,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,EAAH,CAAG,CAAC,CAAA;IAClD,CAAC,CAAC;SACD,IAAI,EAAE,CAAA;AACX,CAAC;AAlBD,oDAkBC"}
|
|
@@ -9,7 +9,7 @@ export interface Mismatch {
|
|
|
9
9
|
seq?: string;
|
|
10
10
|
cliplen?: number;
|
|
11
11
|
}
|
|
12
|
-
export declare function parseCigar(cigar
|
|
12
|
+
export declare function parseCigar(cigar?: string): string[];
|
|
13
13
|
export declare function cigarToMismatches(ops: string[], seq: string, ref?: string, qual?: Buffer): Mismatch[];
|
|
14
14
|
/**
|
|
15
15
|
* parse a SAM MD tag to find mismatching bases of the template versus the reference
|
|
@@ -1,8 +1,8 @@
|
|
|
1
1
|
import { revcom } from '@jbrowse/core/util';
|
|
2
2
|
const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
|
|
3
3
|
const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
|
|
4
|
-
export function parseCigar(cigar) {
|
|
5
|
-
return
|
|
4
|
+
export function parseCigar(cigar = '') {
|
|
5
|
+
return cigar.split(/([MIDNSHPX=])/).slice(0, -1);
|
|
6
6
|
}
|
|
7
7
|
export function cigarToMismatches(ops, seq, ref, qual) {
|
|
8
8
|
let roffset = 0; // reference offset
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"MismatchParser.js","sourceRoot":"","sources":["../../src/BamAdapter/MismatchParser.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAW3C,MAAM,OAAO,GAAG,IAAI,MAAM,CAAC,wBAAwB,CAAC,CAAA;AACpD,MAAM,iBAAiB,GAAG,IAAI,MAAM,CAAC,+BAA+B,CAAC,CAAA;AACrE,MAAM,UAAU,UAAU,CAAC,
|
|
1
|
+
{"version":3,"file":"MismatchParser.js","sourceRoot":"","sources":["../../src/BamAdapter/MismatchParser.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAW3C,MAAM,OAAO,GAAG,IAAI,MAAM,CAAC,wBAAwB,CAAC,CAAA;AACpD,MAAM,iBAAiB,GAAG,IAAI,MAAM,CAAC,+BAA+B,CAAC,CAAA;AACrE,MAAM,UAAU,UAAU,CAAC,KAAK,GAAG,EAAE;IACnC,OAAO,KAAK,CAAC,KAAK,CAAC,eAAe,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;AAClD,CAAC;AACD,MAAM,UAAU,iBAAiB,CAC/B,GAAa,EACb,GAAW,EACX,GAAY,EACZ,IAAa;IAEb,IAAI,OAAO,GAAG,CAAC,CAAA,CAAC,mBAAmB;IACnC,IAAI,OAAO,GAAG,CAAC,CAAA,CAAC,aAAa;IAC7B,MAAM,UAAU,GAAe,EAAE,CAAA;IACjC,MAAM,YAAY,GAAG,GAAG,IAAI,GAAG,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QACtC,MAAM,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;QACnB,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;QAErB,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;YAC1C,IAAI,YAAY,EAAE;gBAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE;oBAC5B;oBACE,sHAAsH;oBACtH,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,KAAK,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,EACjE;wBACA,UAAU,CAAC,IAAI,CAAC;4BACd,KAAK,EAAE,OAAO,GAAG,CAAC;4BAClB,IAAI,EAAE,UAAU;4BAChB,IAAI,EAAE,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC;4BACtB,OAAO,EAAE,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC;4BACzB,MAAM,EAAE,CAAC;yBACV,CAAC,CAAA;qBACH;iBACF;aACF;YACD,OAAO,IAAI,GAAG,CAAA;SACf;QACD,IAAI,EAAE,KAAK,GAAG,EAAE;YACd,UAAU,CAAC,IAAI,CAAC;gBACd,KAAK,EAAE,OAAO;gBACd,IAAI,EAAE,WAAW;gBACjB,IAAI,EAAE,GAAG,GAAG,EAAE;gBACd,MAAM,EAAE,CAAC;aACV,CAAC,CAAA;YACF,OAAO,IAAI,GAAG,CAAA;SACf;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,UAAU,CAAC,IAAI,CAAC;gBACd,KAAK,EAAE,OAAO;gBACd,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,GAAG;gBACT,MAAM,EAAE,GAAG;aACZ,CAAC,CAAA;SACH;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,UAAU,CAAC,IAAI,CAAC;gBACd,KAAK,EAAE,OAAO;gBACd,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,GAAG;gBACT,MAAM,EAAE,GAAG;aACZ,CAAC,CAAA;SACH;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,MAAM,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC,OAAO,EAAE,OAAO,GAAG,GAAG,CAAC,CAAA;YAC3C,MAAM,CAAC,GAAG,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,KAAK,CAAC,OAAO,EAAE,OAAO,GAAG,GAAG,CAAC,KAAI,EAAE,CAAA;YAEnD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE;gBAC5B,UAAU,CAAC,IAAI,CAAC;oBACd,KAAK,EAAE,OAAO,GAAG,CAAC;oBAClB,IAAI,EAAE,UAAU;oBAChB,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;oBACV,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;oBACV,MAAM,EAAE,CAAC;iBACV,CAAC,CAAA;aACH;YACD,OAAO,IAAI,GAAG,CAAA;SACf;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,UAAU,CAAC,IAAI,CAAC;gBACd,KAAK,EAAE,OAAO;gBACd,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,IAAI,GAAG,EAAE;gBACf,OAAO,EAAE,GAAG;gBACZ,MAAM,EAAE,CAAC;aACV,CAAC,CAAA;SACH;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,UAAU,CAAC,IAAI,CAAC;gBACd,KAAK,EAAE,OAAO;gBACd,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,IAAI,GAAG,EAAE;gBACf,OAAO,EAAE,GAAG;gBACZ,MAAM,EAAE,CAAC;aACV,CAAC,CAAA;YACF,OAAO,IAAI,GAAG,CAAA;SACf;QAED,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;YAC1C,OAAO,IAAI,GAAG,CAAA;SACf;KACF;IACD,OAAO,UAAU,CAAA;AACnB,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,cAAc,CAC5B,QAAgB,EAChB,GAAa,EACb,eAA2B,EAC3B,GAAW,EACX,IAAa;IAEb,MAAM,eAAe,GAAe,EAAE,CAAA;IACtC,IAAI,IAAI,GAAa,EAAE,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,IAAI,EAAE,UAAU,EAAE,CAAA;IACxE,MAAM,KAAK,GAAG,eAAe,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,KAAK,MAAM,CAAC,CAAA;IACpE,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,kBAAkB,GAAG,CAAC,CAAA;IAC1B,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,IAAI,WAAW,GAAG,CAAC,CAAA;IAEnB,6DAA6D;IAC7D,8DAA8D;IAC9D,oBAAoB;IAEpB,SAAS,UAAU;QACjB,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAE1B,kCAAkC;QAClC,IAAI,GAAG;YACL,KAAK,EAAE,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,MAAM;YAC/B,MAAM,EAAE,CAAC;YACT,IAAI,EAAE,EAAE;YACR,IAAI,EAAE,UAAU;SACjB,CAAA;IACH,CAAC;IAED,SAAS,qBAAqB,CAAC,QAAgB;QAC7C,IAAI,cAAc,GAAG,kBAAkB,CAAA;QACvC,IAAI,SAAS,GAAG,aAAa,CAAA;QAC7B,KACE,IAAI,CAAC,GAAG,SAAS,EACjB,CAAC,GAAG,GAAG,CAAC,MAAM,IAAI,SAAS,IAAI,QAAQ,EACvC,CAAC,IAAI,CAAC,EAAE,SAAS,GAAG,CAAC,EACrB;YACA,MAAM,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;YAErB,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;gBAC5B,cAAc,IAAI,GAAG,CAAA;aACtB;iBAAM,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;gBACjD,SAAS,IAAI,GAAG,CAAA;aACjB;iBAAM,IAAI,EAAE,KAAK,GAAG,EAAE;gBACrB,cAAc,IAAI,GAAG,CAAA;gBACrB,SAAS,IAAI,GAAG,CAAA;aACjB;SACF;QACD,kBAAkB,GAAG,cAAc,CAAA;QACnC,aAAa,GAAG,SAAS,CAAA;QAEzB,OAAO,cAAc,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAC,CAAA;IAChD,CAAC;IAED,mCAAmC;IACnC,MAAM,EAAE,GAAG,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;IACxC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAClC,MAAM,KAAK,GAAG,EAAE,CAAC,CAAC,CAAC,CAAA;QACnB,MAAM,GAAG,GAAG,CAAC,KAAK,CAAA;QAClB,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE;YACtB,IAAI,CAAC,KAAK,IAAI,GAAG,CAAA;SAClB;aAAM,IAAI,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YAChC,IAAI,CAAC,KAAK,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,CAAA;SAC/B;aAAM;YACL,WAAW;YACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;gBACxC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAA;gBAEf,OAAO,WAAW,GAAG,KAAK,CAAC,MAAM,EAAE;oBACjC,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAA;oBACnC,IAAI,IAAI,CAAC,KAAK,IAAI,QAAQ,CAAC,KAAK,EAAE;wBAChC,IAAI,CAAC,KAAK,IAAI,QAAQ,CAAC,MAAM,CAAA;wBAC7B,WAAW,EAAE,CAAA;qBACd;yBAAM;wBACL,MAAK;qBACN;iBACF;gBACD,MAAM,CAAC,GAAG,qBAAqB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBAC3C,IAAI,CAAC,IAAI,GAAG,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG,CAAA;gBACzB,MAAM,SAAS,GAAG,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAG,CAAC,CAAC,CAAA;gBAC3B,IAAI,SAAS,EAAE;oBACb,IAAI,CAAC,IAAI,GAAG,SAAS,CAAA;iBACtB;gBACD,IAAI,CAAC,OAAO,GAAG,KAAK,CAAA;gBACpB,UAAU,EAAE,CAAA;aACb;SACF;KACF;IACD,OAAO,eAAe,CAAA;AACxB,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,KAAa,EACb,EAAU,EACV,GAAW,EACX,GAAY,EACZ,IAAa;IAEb,IAAI,UAAU,GAAe,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAE7B,oCAAoC;IACpC,IAAI,KAAK,EAAE;QACT,UAAU,GAAG,UAAU,CAAC,MAAM,CAAC,iBAAiB,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,IAAI,CAAC,CAAC,CAAA;KACvE;IAED,2CAA2C;IAC3C,IAAI,EAAE,EAAE;QACN,UAAU,GAAG,UAAU,CAAC,MAAM,CAC5B,cAAc,CAAC,EAAE,EAAE,GAAG,EAAE,UAAU,EAAE,GAAG,EAAE,IAAI,CAAC,CAC/C,CAAA;KACF;IAED,OAAO,UAAU,CAAA;AACnB,CAAC;AACD,4EAA4E;AAC5E,oBAAoB;AACpB,MAAM,SAAS,CAAC,CAAC,aAAa,CAAC,QAAkB,EAAE,SAAmB;IACpE,IAAI,OAAO,GAAG,CAAC,CAAA;IACf,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,OAAO,GAAG,CAAC,CAAA;IAEf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,IAAI,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QACzE,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,EAAE;YAC5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,IAAI,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBAC1D,IAAI,SAAS,CAAC,OAAO,CAAC,KAAK,OAAO,GAAG,CAAC,EAAE;oBACtC,OAAO,EAAE,CAAA;iBACV;aACF;YACD,OAAO,IAAI,GAAG,CAAA;SACf;aAAM,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;YACnC,MAAM,IAAI,GAAG,CAAA;SACd;aAAM,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;YACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,IAAI,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBAC1D,IAAI,SAAS,CAAC,OAAO,CAAC,KAAK,OAAO,GAAG,CAAC,EAAE;oBACtC,MAAM,MAAM,GAAG,CAAC,CAAA;oBAChB,OAAO,EAAE,CAAA;iBACV;aACF;YACD,OAAO,IAAI,GAAG,CAAA;YACd,MAAM,IAAI,GAAG,CAAA;SACd;KACF;AACH,CAAC;AACD,MAAM,UAAU,wBAAwB,CACtC,EAAU,EACV,IAAY,EACZ,OAAe;IAEf,MAAM,GAAG,GAAG,OAAO,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;IAChD,MAAM,IAAI,GAAG,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IAC/C,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACpC,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACnB,MAAM,CAAC,OAAO,EAAE,GAAG,KAAK,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAE1C,8CAA8C;QAC9C,MAAM,OAAO,GAAG,OAAO,CAAC,KAAK,CAAC,iBAAiB,CAAC,CAAA;QAChD,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAA;SACzC;QACD,MAAM,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,GAAG,OAAO,CAAA;QAEzC,oEAAoE;QACpE,kEAAkE;QAClE,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEvD,IAAI,MAAM,KAAK,GAAG,EAAE;YAClB,OAAO,CAAC,IAAI,CAAC,2CAA2C,CAAC,CAAA;YACzD,iEAAiE;YACjE,MAAM,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,SAAS,EAAE,EAAc,EAAE,CAAC,CAAA;SAChE;QAED,qEAAqE;QACrE,wEAAwE;QACxE,wEAAwE;QACxE,IAAI;QACJ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACrC,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACrB,IAAI,CAAC,GAAG,CAAC,CAAA;YACT,MAAM,SAAS,GAAG,EAAE,CAAA;YACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACrC,IAAI,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBACrB,GAAG;oBACD,IAAI,IAAI,KAAK,GAAG,IAAI,IAAI,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE;wBACnC,KAAK,EAAE,CAAA;qBACR;oBACD,CAAC,EAAE,CAAA;iBACJ,QAAQ,KAAK,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,CAAC,MAAM,EAAC;gBAEtC,MAAM,IAAI,GAAG,CAAC,GAAG,CAAC,CAAA;gBAClB,SAAS,CAAC,IAAI,CAAC,OAAO,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;aAC9D;YACD,IAAI,OAAO,KAAK,CAAC,CAAC,EAAE;gBAClB,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;aAChC;YACD,MAAM,CAAC,IAAI,CAAC;gBACV,IAAI;gBACJ,SAAS;aACV,CAAC,CAAA;SACH;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,EAAU;IAC7C,MAAM,IAAI,GAAG,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IAC1B,OAAO,IAAI;SACR,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;SACpB,GAAG,CAAC,GAAG,CAAC,EAAE;QACT,MAAM,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAEhC,MAAM,OAAO,GAAG,OAAO,CAAC,KAAK,CAAC,iBAAiB,CAAC,CAAA;QAChD,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAA;SACzC;QACD,MAAM,CAAC,EAAE,AAAD,EAAG,AAAD,EAAG,OAAO,CAAC,GAAG,OAAO,CAAA;QAE/B,oEAAoE;QACpE,kEAAkE;QAClE,OAAO,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAClD,CAAC,CAAC;SACD,IAAI,EAAE,CAAA;AACX,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-alignments",
|
|
3
|
-
"version": "2.0.
|
|
3
|
+
"version": "2.0.1",
|
|
4
4
|
"description": "JBrowse 2 alignments adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -47,9 +47,9 @@
|
|
|
47
47
|
"generic-filehandle": "^2.2.2"
|
|
48
48
|
},
|
|
49
49
|
"peerDependencies": {
|
|
50
|
-
"@jbrowse/core": "^
|
|
51
|
-
"@jbrowse/plugin-linear-genome-view": "^
|
|
52
|
-
"@jbrowse/plugin-wiggle": "^
|
|
50
|
+
"@jbrowse/core": "^2.0.0",
|
|
51
|
+
"@jbrowse/plugin-linear-genome-view": "^2.0.0",
|
|
52
|
+
"@jbrowse/plugin-wiggle": "^2.0.0",
|
|
53
53
|
"@mui/material": "^5.0.0",
|
|
54
54
|
"mobx": "^6.0.0",
|
|
55
55
|
"mobx-react": "^7.0.0",
|
|
@@ -65,5 +65,5 @@
|
|
|
65
65
|
"distModule": "esm/index.js",
|
|
66
66
|
"srcModule": "src/index.ts",
|
|
67
67
|
"module": "esm/index.js",
|
|
68
|
-
"gitHead": "
|
|
68
|
+
"gitHead": "ed935bf5612af3818abdc8ef52d100d5d81d33a2"
|
|
69
69
|
}
|
|
@@ -11,8 +11,8 @@ export interface Mismatch {
|
|
|
11
11
|
}
|
|
12
12
|
const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi)
|
|
13
13
|
const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/)
|
|
14
|
-
export function parseCigar(cigar
|
|
15
|
-
return
|
|
14
|
+
export function parseCigar(cigar = '') {
|
|
15
|
+
return cigar.split(/([MIDNSHPX=])/).slice(0, -1)
|
|
16
16
|
}
|
|
17
17
|
export function cigarToMismatches(
|
|
18
18
|
ops: string[],
|