@gmod/bam 1.1.13 → 1.1.16

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.
Files changed (30) hide show
  1. package/CHANGELOG.md +16 -1
  2. package/dist/bamFile.d.ts +3 -2
  3. package/dist/bamFile.js +209 -224
  4. package/dist/bamFile.js.map +1 -1
  5. package/dist/csi.js +5 -1
  6. package/dist/csi.js.map +1 -1
  7. package/dist/htsget.js +5 -1
  8. package/dist/htsget.js.map +1 -1
  9. package/dist/record.js +20 -19
  10. package/dist/record.js.map +1 -1
  11. package/esm/bamFile.d.ts +3 -2
  12. package/esm/bamFile.js +76 -87
  13. package/esm/bamFile.js.map +1 -1
  14. package/esm/record.js +19 -18
  15. package/esm/record.js.map +1 -1
  16. package/package.json +12 -8
  17. package/src/bai.ts +227 -0
  18. package/src/bamFile.ts +546 -0
  19. package/src/chunk.ts +52 -0
  20. package/src/constants.ts +26 -0
  21. package/src/csi.ts +246 -0
  22. package/src/declare.d.ts +2 -0
  23. package/src/errors.ts +22 -0
  24. package/src/htsget.ts +138 -0
  25. package/src/index.ts +7 -0
  26. package/src/indexFile.ts +63 -0
  27. package/src/record.ts +610 -0
  28. package/src/sam.ts +15 -0
  29. package/src/util.ts +116 -0
  30. package/src/virtualOffset.ts +47 -0
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/csi.js CHANGED
@@ -16,7 +16,11 @@ var __extends = (this && this.__extends) || (function () {
16
16
  })();
17
17
  var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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18
  if (k2 === undefined) k2 = k;
19
- Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
19
+ var desc = Object.getOwnPropertyDescriptor(m, k);
20
+ if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
21
+ desc = { enumerable: true, get: function() { return m[k]; } };
22
+ }
23
+ Object.defineProperty(o, k2, desc);
20
24
  }) : (function(o, m, k, k2) {
21
25
  if (k2 === undefined) k2 = k;
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26
  o[k2] = m[k];
package/dist/csi.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/htsget.js CHANGED
@@ -27,7 +27,11 @@ var __assign = (this && this.__assign) || function () {
27
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  };
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28
  var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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  if (k2 === undefined) k2 = k;
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- Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
30
+ var desc = Object.getOwnPropertyDescriptor(m, k);
31
+ if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
32
+ desc = { enumerable: true, get: function() { return m[k]; } };
33
+ }
34
+ Object.defineProperty(o, k2, desc);
31
35
  }) : (function(o, m, k, k2) {
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36
  if (k2 === undefined) k2 = k;
33
37
  o[k2] = m[k];
package/dist/htsget.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,mDAA8C;AAC9C,gCAA6B;AAE7B,yDAA6C;AAC7C,6BAAuC;AAWvC,SAAe,MAAM,CAAC,GAAsB,EAAE,IAAyB;;;;;;wBACzD,qBAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,UAAO,KAAkB;;;;;oCACvB,GAAG,GAAc,KAAK,IAAnB,EAAE,OAAO,GAAK,KAAK,QAAV,CAAU;yCAC1B,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAvB,wBAAuB;oCACzB,sBAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,EAAA;;oCAKvC,OAAO,GAAc,OAAO,QAArB,EAAK,IAAI,UAAK,OAAO,EAA9B,WAAoB,CAAF,CAAY;oCACxB,qBAAM,KAAK,CAAC,GAAG,wBACtB,IAAI,KACP,OAAO,wBAAO,IAAI,CAAC,OAAO,GAAK,IAAI,KACnC,EAAA;;oCAHI,QAAM,SAGV;oCACF,IAAI,CAAC,KAAG,CAAC,EAAE,EAAE;wCACX,MAAM,IAAI,KAAK,CAAC,0BAAmB,KAAG,CAAC,UAAU,CAAE,CAAC,CAAA;qCACrD;oCACM,KAAA,CAAA,KAAA,MAAM,CAAA,CAAC,IAAI,CAAA;oCAAC,qBAAM,KAAG,CAAC,WAAW,EAAE,EAAA;wCAA1C,sBAAO,cAAY,SAAuB,EAAC,EAAA;;;yBAE9C,CAAC,CACH,EAAA;;oBApBK,GAAG,GAAG,SAoBX;oBAEM,KAAA,CAAA,KAAA,MAAM,CAAA,CAAC,MAAM,CAAA;oBAAC,qBAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,UAAA,GAAG,IAAI,OAAA,IAAA,uBAAK,EAAC,GAAG,CAAC,EAAV,CAAU,CAAC,CAAC,EAAA;wBAAlE,sBAAO,cAAc,SAA6C,EAAC,EAAA;;;;CACpE;AAED;IAAwC,8BAAO;IAK7C,oBAAY,IAA0C;QAAtD;QACE,mCAAmC;QACnC,kBAAM,EAAE,aAAa,EAAE,GAAG,EAAE,aAAa,EAAE,GAAG,EAAE,CAAC,SAGlD;QAFC,KAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,KAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;;IAC7B,CAAC;IAEM,0CAAqB,GAA5B,UACE,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAIC;QAJD,qBAAA,EAAA;YACE,WAAW,EAAE,KAAK;YAClB,aAAa,EAAE,KAAK;YACpB,aAAa,EAAE,MAAM;SACtB;;;;;;wBAEK,IAAI,GAAG,UAAG,IAAI,CAAC,OAAO,cAAI,IAAI,CAAC,OAAO,CAAE,CAAA;wBACxC,GAAG,GAAG,UAAG,IAAI,4BAAkB,GAAG,oBAAU,GAAG,kBAAQ,GAAG,gBAAa,CAAA;wBACvE,KAAK,GAAG,IAAI,CAAC,UAAU,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;wBACtC,6BAAM,KAAK,CAAC,GAAG,eAAO,IAAI,EAAG,GAAA;;wBAAtC,MAAM,GAAG,SAA6B;wBAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;4BACd,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;yBACnC;wBACY,6BAAM,MAAM,CAAC,IAAI,EAAE,GAAA;;wBAA1B,IAAI,GAAG,SAAmB;wBAClB,6BAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAA;;wBAArD,KAAK,GAAG,SAA6C;wBACrD,KAAK,GAAG;4BACZ,MAAM,EAAE,KAAK;4BACb,KAAK,EAAE,EAAE,IAAI,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,EAAE;4BACpC,QAAQ;gCACN,OAAO,UAAG,GAAG,cAAI,GAAG,cAAI,GAAG,CAAE,CAAA;4BAC/B,CAAC;yBACF,CAAA;wBAED,sBAAA,SAAO,iBAAA,cAAA,IAAI,CAAC,mBAAmB;4BAC7B,aAAa;4BACb,CAAC,KAAK,CAAC,EACP,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA,CAAA,CAAA,EAAA;4BAPD,4CAAA,SAOC,IAAA;;wBAPD,SAOC,CAAA;;;;;KACF;IAED,YAAY;IACN,+BAAU,GAAhB,UAAiB,MAGhB;;;;gBACS,KAAK,GAAK,MAAM,MAAX,CAAW;gBAChB,MAAM,GAAgB,KAAK,OAArB,EAAS,EAAE,GAAK,KAAK,MAAV,CAAU;gBACnC,sBAAO,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,EAAA;;;KACvE;IAEK,8BAAS,GAAf,UAAgB,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;;;wBAC3B,GAAG,GAAG,UAAG,IAAI,CAAC,OAAO,cAAI,IAAI,CAAC,OAAO,mCAAgC,CAAA;wBAC5D,qBAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,EAAA;;wBAA/B,MAAM,GAAG,SAAsB;wBACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;4BACd,MAAM,IAAI,KAAK,CAAC,0BAAmB,MAAM,CAAC,UAAU,CAAE,CAAC,CAAA;yBACxD;wBACY,qBAAM,MAAM,CAAC,IAAI,EAAE,EAAA;;wBAA1B,IAAI,GAAG,SAAmB;wBAClB,qBAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,EAAA;;wBAA5C,KAAK,GAAG,SAAoC;wBAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,mBAAS,EAAE;4BACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;yBAClC;wBACK,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBAE9B,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;wBACnD,SAAS,GAAG,IAAA,qBAAe,EAAC,UAAU,CAAC,CAAA;wBAIvC,QAAQ,GAAa,EAAE,CAAA;wBACvB,QAAQ,GAA2B,EAAE,CAAA;wBACrC,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,UAAC,CAAkB,IAAK,OAAA,CAAC,CAAC,GAAG,KAAK,IAAI,EAAd,CAAc,CAAC,CAAA;wBACxE,OAAO,CAAC,OAAO,CAAC,UAAC,MAA8B,EAAE,KAAa;4BAC5D,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,UAAC,IAAgB;gCACnC,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oCACrB,uBAAuB;oCACvB,IAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;oCAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;oCACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;iCAC1B;4BACH,CAAC,CAAC,CAAA;wBACJ,CAAC,CAAC,CAAA;wBACF,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;wBAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;wBAC1B,sBAAO,SAAS,EAAA;;;;KACjB;IACH,iBAAC;AAAD,CAAC,AA/FD,CAAwC,iBAAO,GA+F9C"}
1
+ {"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,mDAA8C;AAC9C,gCAA6B;AAE7B,yDAA6C;AAC7C,6BAAuC;AAWvC,SAAe,MAAM,CAAC,GAAsB,EAAE,IAAyB;;;;;;wBACzD,qBAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,UAAO,KAAkB;;;;;oCACvB,GAAG,GAAc,KAAK,IAAnB,EAAE,OAAO,GAAK,KAAK,QAAV,CAAU;yCAC1B,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAvB,wBAAuB;oCACzB,sBAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,EAAA;;oCAKvC,OAAO,GAAc,OAAO,QAArB,EAAK,IAAI,UAAK,OAAO,EAA9B,WAAoB,CAAF,CAAY;oCACxB,qBAAM,KAAK,CAAC,GAAG,wBACtB,IAAI,KACP,OAAO,wBAAO,IAAI,CAAC,OAAO,GAAK,IAAI,KACnC,EAAA;;oCAHI,QAAM,SAGV;oCACF,IAAI,CAAC,KAAG,CAAC,EAAE,EAAE;wCACX,MAAM,IAAI,KAAK,CAAC,0BAAmB,KAAG,CAAC,UAAU,CAAE,CAAC,CAAA;qCACrD;oCACM,KAAA,CAAA,KAAA,MAAM,CAAA,CAAC,IAAI,CAAA;oCAAC,qBAAM,KAAG,CAAC,WAAW,EAAE,EAAA;wCAA1C,sBAAO,cAAY,SAAuB,EAAC,EAAA;;;yBAE9C,CAAC,CACH,EAAA;;oBApBK,GAAG,GAAG,SAoBX;oBAEM,KAAA,CAAA,KAAA,MAAM,CAAA,CAAC,MAAM,CAAA;oBAAC,qBAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,UAAA,GAAG,IAAI,OAAA,IAAA,uBAAK,EAAC,GAAG,CAAC,EAAV,CAAU,CAAC,CAAC,EAAA;wBAAlE,sBAAO,cAAc,SAA6C,EAAC,EAAA;;;;CACpE;AAED;IAAwC,8BAAO;IAK7C,oBAAY,IAA0C;QAAtD;QACE,mCAAmC;QACnC,kBAAM,EAAE,aAAa,EAAE,GAAG,EAAE,aAAa,EAAE,GAAG,EAAE,CAAC,SAGlD;QAFC,KAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,KAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;;IAC7B,CAAC;IAEM,0CAAqB,GAA5B,UACE,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAIC;QAJD,qBAAA,EAAA;YACE,WAAW,EAAE,KAAK;YAClB,aAAa,EAAE,KAAK;YACpB,aAAa,EAAE,MAAM;SACtB;;;;;;wBAEK,IAAI,GAAG,UAAG,IAAI,CAAC,OAAO,cAAI,IAAI,CAAC,OAAO,CAAE,CAAA;wBACxC,GAAG,GAAG,UAAG,IAAI,4BAAkB,GAAG,oBAAU,GAAG,kBAAQ,GAAG,gBAAa,CAAA;wBACvE,KAAK,GAAG,IAAI,CAAC,UAAU,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;wBACtC,6BAAM,KAAK,CAAC,GAAG,eAAO,IAAI,EAAG,GAAA;;wBAAtC,MAAM,GAAG,SAA6B;wBAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;4BACd,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;yBACnC;wBACY,6BAAM,MAAM,CAAC,IAAI,EAAE,GAAA;;wBAA1B,IAAI,GAAG,SAAmB;wBAClB,6BAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAA;;wBAArD,KAAK,GAAG,SAA6C;wBACrD,KAAK,GAAG;4BACZ,MAAM,EAAE,KAAK;4BACb,KAAK,EAAE,EAAE,IAAI,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,EAAE;4BACpC,QAAQ;gCACN,OAAO,UAAG,GAAG,cAAI,GAAG,cAAI,GAAG,CAAE,CAAA;4BAC/B,CAAC;yBACF,CAAA;wBAED,sBAAA,SAAO,iBAAA,cAAA,IAAI,CAAC,mBAAmB;4BAC7B,aAAa;4BACb,CAAC,KAAK,CAAC,EACP,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA,CAAA,CAAA,EAAA;4BAPD,4CAAA,SAOC,IAAA;;wBAPD,SAOC,CAAA;;;;;KACF;IAED,YAAY;IACN,+BAAU,GAAhB,UAAiB,MAGhB;;;;gBACS,KAAK,GAAK,MAAM,MAAX,CAAW;gBAChB,MAAM,GAAgB,KAAK,OAArB,EAAS,EAAE,GAAK,KAAK,MAAV,CAAU;gBACnC,sBAAO,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,EAAA;;;KACvE;IAEK,8BAAS,GAAf,UAAgB,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;;;wBAC3B,GAAG,GAAG,UAAG,IAAI,CAAC,OAAO,cAAI,IAAI,CAAC,OAAO,mCAAgC,CAAA;wBAC5D,qBAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,EAAA;;wBAA/B,MAAM,GAAG,SAAsB;wBACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;4BACd,MAAM,IAAI,KAAK,CAAC,0BAAmB,MAAM,CAAC,UAAU,CAAE,CAAC,CAAA;yBACxD;wBACY,qBAAM,MAAM,CAAC,IAAI,EAAE,EAAA;;wBAA1B,IAAI,GAAG,SAAmB;wBAClB,qBAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,EAAA;;wBAA5C,KAAK,GAAG,SAAoC;wBAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,mBAAS,EAAE;4BACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;yBAClC;wBACK,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBAE9B,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;wBACnD,SAAS,GAAG,IAAA,qBAAe,EAAC,UAAU,CAAC,CAAA;wBAIvC,QAAQ,GAAa,EAAE,CAAA;wBACvB,QAAQ,GAA2B,EAAE,CAAA;wBACrC,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,UAAC,CAAkB,IAAK,OAAA,CAAC,CAAC,GAAG,KAAK,IAAI,EAAd,CAAc,CAAC,CAAA;wBACxE,OAAO,CAAC,OAAO,CAAC,UAAC,MAA8B,EAAE,KAAa;4BAC5D,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,UAAC,IAAgB;gCACnC,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oCACrB,uBAAuB;oCACvB,IAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;oCAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;oCACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;iCAC1B;4BACH,CAAC,CAAC,CAAA;wBACJ,CAAC,CAAC,CAAA;wBACF,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;wBAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;wBAC1B,sBAAO,SAAS,EAAA;;;;KACjB;IACH,iBAAC;AAAD,CAAC,AA/FD,CAAwC,iBAAO,GA+F9C"}
package/dist/record.js CHANGED
@@ -38,8 +38,7 @@ var BamRecord = /** @class */ (function () {
38
38
  return this._get(field.toLowerCase());
39
39
  };
40
40
  BamRecord.prototype.end = function () {
41
- return (this.get('start') +
42
- (this.get('length_on_ref') || this.get('seq_length') || undefined));
41
+ return this.get('start') + this.get('length_on_ref');
43
42
  };
44
43
  BamRecord.prototype.seq_id = function () {
45
44
  return this._refID;
@@ -425,9 +424,13 @@ var BamRecord = /** @class */ (function () {
425
424
  };
426
425
  BamRecord.prototype._flags = function () { };
427
426
  BamRecord.prototype.length_on_ref = function () {
428
- this.get('cigar'); // the length_on_ref is set as a
429
- // side effect of the CIGAR parsing
430
- return this.data.length_on_ref;
427
+ if (this.data.length_on_ref) {
428
+ return this.data.length_on_ref;
429
+ }
430
+ else {
431
+ this.get('cigar'); // the length_on_ref is set as a side effect
432
+ return this.data.length_on_ref;
433
+ }
431
434
  };
432
435
  BamRecord.prototype._n_cigar_op = function () {
433
436
  return this.get('_flag_nc') & 0xffff;
@@ -445,24 +448,22 @@ var BamRecord = /** @class */ (function () {
445
448
  return this.seq();
446
449
  };
447
450
  BamRecord.prototype.seq = function () {
448
- var _a = this.bytes, start = _a.start, byteArray = _a.byteArray;
451
+ var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
449
452
  var p = start + 36 + this.get('_l_read_name') + this.get('_n_cigar_op') * 4;
450
453
  var seqBytes = this.get('_seq_bytes');
451
454
  var len = this.get('seq_length');
452
- var buf = [];
453
- for (var j = 0; j < seqBytes - 1; ++j) {
454
- var sb_1 = byteArray[p + j];
455
- buf.push(SEQRET_DECODER[(sb_1 & 0xf0) >> 4]);
456
- buf.push(SEQRET_DECODER[sb_1 & 0x0f]);
457
- }
458
- // there are two bases per byte, so this handles the case where it is odd
459
- // length
460
- var sb = byteArray[p + seqBytes - 1];
461
- buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
462
- if (len % 2 === 0) {
463
- buf.push(SEQRET_DECODER[sb & 0x0f]);
455
+ var buf = '';
456
+ var i = 0;
457
+ for (var j = 0; j < seqBytes; ++j) {
458
+ var sb = byteArray[p + j];
459
+ buf += SEQRET_DECODER[(sb & 0xf0) >> 4];
460
+ i++;
461
+ if (i < len) {
462
+ buf += SEQRET_DECODER[sb & 0x0f];
463
+ i++;
464
+ }
464
465
  }
465
- return buf.join('');
466
+ return buf;
466
467
  };
467
468
  // adapted from igv.js
468
469
  BamRecord.prototype.getPairOrientation = function () {
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/bamFile.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  /// <reference types="node" />
2
- import Chunk from './chunk';
3
2
  import { GenericFilehandle } from 'generic-filehandle';
3
+ import Chunk from './chunk';
4
4
  import BAMFeature from './record';
5
5
  import { BamOpts, BaseOpts } from './util';
6
6
  export declare const BAM_MAGIC = 21840194;
@@ -14,6 +14,7 @@ export default class BamFile {
14
14
  protected chrToIndex: any;
15
15
  protected indexToChr: any;
16
16
  private yieldThreadTime;
17
+ private featureCache;
17
18
  /**
18
19
  * @param {object} args
19
20
  * @param {string} [args.bamPath]
@@ -56,7 +57,7 @@ export default class BamFile {
56
57
  getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
57
58
  streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
58
59
  _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
59
- fetchPairs(chrId: number, featPromises: Promise<BAMFeature[]>[], opts: BamOpts): Promise<BAMFeature[]>;
60
+ fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
60
61
  _readChunk({ chunk, opts }: {
61
62
  chunk: Chunk;
62
63
  opts: BaseOpts;
package/esm/bamFile.js CHANGED
@@ -1,14 +1,27 @@
1
- import BAI from './bai';
2
- import CSI from './csi';
3
1
  import crc32 from 'buffer-crc32';
4
2
  import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
5
3
  import entries from 'object.entries-ponyfill';
6
4
  import { LocalFile, RemoteFile } from 'generic-filehandle';
5
+ import AbortablePromiseCache from 'abortable-promise-cache';
6
+ import QuickLRU from 'quick-lru';
7
+ //locals
8
+ import BAI from './bai';
9
+ import CSI from './csi';
7
10
  import BAMFeature from './record';
8
11
  import { parseHeaderText } from './sam';
9
12
  import { abortBreakPoint, checkAbortSignal, timeout, makeOpts, } from './util';
10
13
  export const BAM_MAGIC = 21840194;
11
14
  const blockLen = 1 << 16;
15
+ function flat(arr) {
16
+ return [].concat(...arr);
17
+ }
18
+ async function gen2array(gen) {
19
+ const out = [];
20
+ for await (const x of gen) {
21
+ out.push(x);
22
+ }
23
+ return out;
24
+ }
12
25
  export default class BamFile {
13
26
  /**
14
27
  * @param {object} args
@@ -18,6 +31,21 @@ export default class BamFile {
18
31
  * @param {FileHandle} [args.baiFilehandle]
19
32
  */
20
33
  constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, fetchSizeLimit, chunkSizeLimit, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
34
+ this.featureCache = new AbortablePromiseCache({
35
+ //@ts-ignore
36
+ cache: new QuickLRU({
37
+ maxSize: 50,
38
+ }),
39
+ //@ts-ignore
40
+ fill: async ({ chunk, opts }, signal) => {
41
+ const { data, cpositions, dpositions } = await this._readChunk({
42
+ chunk,
43
+ opts: { ...opts, signal },
44
+ });
45
+ const feats = await this.readBamFeatures(data, cpositions, dpositions, chunk);
46
+ return feats;
47
+ },
48
+ });
21
49
  this.renameRefSeq = renameRefSeqs;
22
50
  if (bamFilehandle) {
23
51
  this.bam = bamFilehandle;
@@ -101,31 +129,23 @@ export default class BamFile {
101
129
  await this.getHeader(opts);
102
130
  return this.header;
103
131
  }
104
- // the full length of the refseq block is not given in advance so this grabs a chunk and
105
- // doubles it if all refseqs haven't been processed
132
+ // the full length of the refseq block is not given in advance so this grabs
133
+ // a chunk and doubles it if all refseqs haven't been processed
106
134
  async _readRefSeqs(start, refSeqBytes, opts = {}) {
107
135
  if (start > refSeqBytes) {
108
136
  return this._readRefSeqs(start, refSeqBytes * 2, opts);
109
137
  }
110
- const res = await this.bam.read(Buffer.alloc(refSeqBytes + blockLen), 0, refSeqBytes, 0, opts);
111
- const { bytesRead } = res;
112
- let { buffer } = res;
138
+ const size = refSeqBytes + blockLen;
139
+ const { bytesRead, buffer } = await this.bam.read(Buffer.alloc(size), 0, refSeqBytes, 0, opts);
113
140
  if (!bytesRead) {
114
141
  throw new Error('Error reading refseqs from header');
115
142
  }
116
- if (bytesRead < refSeqBytes) {
117
- buffer = buffer.subarray(0, bytesRead);
118
- }
119
- else {
120
- buffer = buffer.subarray(0, refSeqBytes);
121
- }
122
- const uncba = await unzip(buffer);
143
+ const uncba = await unzip(buffer.subarray(0, Math.min(bytesRead, refSeqBytes)));
123
144
  const nRef = uncba.readInt32LE(start);
124
145
  let p = start + 4;
125
146
  const chrToIndex = {};
126
147
  const indexToChr = [];
127
148
  for (let i = 0; i < nRef; i += 1) {
128
- await abortBreakPoint(opts.signal);
129
149
  const lName = uncba.readInt32LE(p);
130
150
  const refName = this.renameRefSeq(uncba.toString('utf8', p + 4, p + 4 + lName - 1));
131
151
  const lRef = uncba.readInt32LE(p + lName + 4);
@@ -144,11 +164,7 @@ export default class BamFile {
144
164
  pairAcrossChr: false,
145
165
  maxInsertSize: 200000,
146
166
  }) {
147
- let records = [];
148
- for await (const chunk of this.streamRecordsForRange(chr, min, max, opts)) {
149
- records = records.concat(chunk);
150
- }
151
- return records;
167
+ return flat(await gen2array(this.streamRecordsForRange(chr, min, max, opts)));
152
168
  }
153
169
  async *streamRecordsForRange(chr, min, max, opts = {}) {
154
170
  const { signal } = opts;
@@ -180,52 +196,45 @@ export default class BamFile {
180
196
  }
181
197
  async *_fetchChunkFeatures(chunks, chrId, min, max, opts) {
182
198
  const { viewAsPairs = false } = opts;
183
- const featPromises = [];
199
+ const feats = [];
184
200
  let done = false;
185
201
  for (let i = 0; i < chunks.length; i++) {
186
- const { data, cpositions, dpositions, chunk } = await this._readChunk({
187
- chunk: chunks[i],
202
+ const c = chunks[i];
203
+ const records = (await this.featureCache.get(c.toString(), {
204
+ chunk: c,
188
205
  opts,
189
- });
190
- const promise = this.readBamFeatures(data, cpositions, dpositions, chunk).then(records => {
191
- const recs = [];
192
- for (let i = 0; i < records.length; i += 1) {
193
- const feature = records[i];
194
- if (feature.seq_id() === chrId) {
195
- if (feature.get('start') >= max) {
196
- // past end of range, can stop iterating
197
- done = true;
198
- break;
199
- }
200
- else if (feature.get('end') >= min) {
201
- // must be in range
202
- recs.push(feature);
203
- }
206
+ }, opts.signal));
207
+ const recs = [];
208
+ for (let i = 0; i < records.length; i += 1) {
209
+ const feature = records[i];
210
+ if (feature.seq_id() === chrId) {
211
+ if (feature.get('start') >= max) {
212
+ // past end of range, can stop iterating
213
+ done = true;
214
+ break;
215
+ }
216
+ else if (feature.get('end') >= min) {
217
+ // must be in range
218
+ recs.push(feature);
204
219
  }
205
220
  }
206
- return recs;
207
- });
208
- featPromises.push(promise);
209
- await promise;
221
+ }
222
+ feats.push(recs);
223
+ yield recs;
210
224
  if (done) {
211
225
  break;
212
226
  }
213
227
  }
214
228
  checkAbortSignal(opts.signal);
215
- for (let i = 0; i < featPromises.length; i++) {
216
- yield featPromises[i];
217
- }
218
- checkAbortSignal(opts.signal);
219
229
  if (viewAsPairs) {
220
- yield this.fetchPairs(chrId, featPromises, opts);
230
+ yield this.fetchPairs(chrId, feats, opts);
221
231
  }
222
232
  }
223
- async fetchPairs(chrId, featPromises, opts) {
233
+ async fetchPairs(chrId, feats, opts) {
224
234
  const { pairAcrossChr = false, maxInsertSize = 200000 } = opts;
225
235
  const unmatedPairs = {};
226
236
  const readIds = {};
227
- await Promise.all(featPromises.map(async (f) => {
228
- const ret = await f;
237
+ feats.map(ret => {
229
238
  const readNames = {};
230
239
  for (let i = 0; i < ret.length; i++) {
231
240
  const name = ret[i].name();
@@ -241,29 +250,25 @@ export default class BamFile {
241
250
  unmatedPairs[k] = true;
242
251
  }
243
252
  });
244
- }));
253
+ });
245
254
  const matePromises = [];
246
- await Promise.all(featPromises.map(async (f) => {
247
- const ret = await f;
255
+ feats.map(ret => {
248
256
  for (let i = 0; i < ret.length; i++) {
249
- const name = ret[i].name();
257
+ const f = ret[i];
258
+ const name = f.name();
259
+ const start = f.get('start');
260
+ const pnext = f._next_pos();
261
+ const rnext = f._next_refid();
250
262
  if (unmatedPairs[name] &&
251
263
  (pairAcrossChr ||
252
- (ret[i]._next_refid() === chrId &&
253
- Math.abs(ret[i].get('start') - ret[i]._next_pos()) <
254
- maxInsertSize))) {
255
- matePromises.push(this.index.blocksForRange(ret[i]._next_refid(), ret[i]._next_pos(), ret[i]._next_pos() + 1, opts));
264
+ (rnext === chrId && Math.abs(start - pnext) < maxInsertSize))) {
265
+ matePromises.push(this.index.blocksForRange(rnext, pnext, pnext + 1, opts));
256
266
  }
257
267
  }
258
- }));
259
- const mateBlocks = await Promise.all(matePromises);
260
- let mateChunks = [];
261
- for (let i = 0; i < mateBlocks.length; i++) {
262
- mateChunks = mateChunks.concat(mateBlocks[i]);
263
- }
268
+ });
264
269
  // filter out duplicate chunks (the blocks are lists of chunks, blocks are
265
270
  // concatenated, then filter dup chunks)
266
- mateChunks = mateChunks
271
+ const mateChunks = flat(await Promise.all(matePromises))
267
272
  .sort()
268
273
  .filter((item, pos, ary) => !pos || item.toString() !== ary[pos - 1].toString());
269
274
  const mateTotalSize = mateChunks
@@ -287,29 +292,12 @@ export default class BamFile {
287
292
  }
288
293
  return mateRecs;
289
294
  });
290
- const newMateFeats = await Promise.all(mateFeatPromises);
291
- let featuresRet = [];
292
- if (newMateFeats.length) {
293
- const newMates = newMateFeats.reduce((result, current) => result.concat(current));
294
- featuresRet = featuresRet.concat(newMates);
295
- }
296
- return featuresRet;
295
+ return flat(await Promise.all(mateFeatPromises));
297
296
  }
298
297
  async _readChunk({ chunk, opts }) {
299
- const { signal } = opts;
300
- const bufsize = chunk.fetchedSize();
301
- const res = await this.bam.read(Buffer.alloc(bufsize), 0, bufsize, chunk.minv.blockPosition, opts);
302
- const { bytesRead } = res;
303
- let { buffer } = res;
304
- checkAbortSignal(signal);
305
- if (bytesRead < bufsize) {
306
- buffer = buffer.subarray(0, bytesRead);
307
- }
308
- else {
309
- buffer = buffer.subarray(0, bufsize);
310
- }
311
- const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buffer, chunk);
312
- checkAbortSignal(signal);
298
+ const size = chunk.fetchedSize();
299
+ const { buffer, bytesRead } = await this.bam.read(Buffer.alloc(size), 0, size, chunk.minv.blockPosition, opts);
300
+ const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buffer.subarray(0, Math.min(bytesRead, size)), chunk);
313
301
  return { data, cpositions, dpositions, chunk };
314
302
  }
315
303
  async readBamFeatures(ba, cpositions, dpositions, chunk) {
@@ -354,7 +342,8 @@ export default class BamFile {
354
342
  (blockStart - dpositions[pos]) +
355
343
  chunk.minv.dataPosition +
356
344
  1
357
- : crc32.signed(ba.subarray(blockStart, blockEnd)),
345
+ : // must be slice, not subarray for buffer polyfill on web
346
+ crc32.signed(ba.slice(blockStart, blockEnd)),
358
347
  });
359
348
  sink.push(feature);
360
349
  if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {