npm - @gmod/cram - Versions diffs - 2.0.0 → 2.0.2 - Mend

@gmod/cram 2.0.0 → 2.0.2

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 (143) hide show

package/CHANGELOG.md +4 -0
package/dist/craiIndex.d.ts +2 -2
package/dist/craiIndex.js +5 -9
package/dist/craiIndex.js.map +1 -1
package/dist/cram-bundle.js +1 -1
package/dist/cramFile/codecs/_base.d.ts +6 -6
package/dist/cramFile/codecs/beta.js.map +1 -1
package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
package/dist/cramFile/codecs/external.js +1 -0
package/dist/cramFile/codecs/external.js.map +1 -1
package/dist/cramFile/codecs/gamma.js.map +1 -1
package/dist/cramFile/codecs/getBits.js.map +1 -1
package/dist/cramFile/codecs/huffman.d.ts +0 -1
package/dist/cramFile/codecs/huffman.js +1 -3
package/dist/cramFile/codecs/huffman.js.map +1 -1
package/dist/cramFile/codecs/index.js.map +1 -1
package/dist/cramFile/codecs/subexp.js.map +1 -1
package/dist/cramFile/container/compressionScheme.js +1 -1
package/dist/cramFile/container/compressionScheme.js.map +1 -1
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/encoding.d.ts +20 -20
package/dist/cramFile/file.d.ts +14 -7
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/filehandle.d.ts +1 -2
package/dist/cramFile/index.d.ts +1 -2
package/dist/cramFile/index.js +3 -3
package/dist/cramFile/index.js.map +1 -1
package/dist/cramFile/record.d.ts +6 -6
package/dist/cramFile/record.js +7 -4
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/sectionParsers.d.ts +9 -8
package/dist/cramFile/sectionParsers.js +10 -11
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +7 -11
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.js +24 -22
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.d.ts +1 -0
package/dist/cramFile/util.js +1 -1
package/dist/cramFile/util.js.map +1 -1
package/dist/index.d.ts +3 -4
package/dist/index.js +7 -30
package/dist/index.js.map +1 -1
package/dist/indexedCramFile.d.ts +6 -6
package/dist/indexedCramFile.js +13 -18
package/dist/indexedCramFile.js.map +1 -1
package/dist/io/index.d.ts +2 -1
package/dist/io/index.js +4 -3
package/dist/io/index.js.map +1 -1
package/dist/rans/d04.js.map +1 -1
package/dist/rans/d14.js.map +1 -1
package/dist/rans/decoding.js.map +1 -1
package/dist/rans/frequencies.js.map +1 -1
package/dist/rans/index.js.map +1 -1
package/dist/sam.d.ts +5 -6
package/dist/sam.js +20 -7
package/dist/sam.js.map +1 -1
package/dist/typescript.js.map +1 -1
package/dist/unzip.d.ts +2 -2
package/dist/unzip.js +1 -1
package/dist/unzip.js.map +1 -1
package/esm/craiIndex.d.ts +2 -2
package/esm/craiIndex.js +5 -9
package/esm/craiIndex.js.map +1 -1
package/esm/cramFile/codecs/_base.d.ts +6 -6
package/esm/cramFile/codecs/beta.js.map +1 -1
package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
package/esm/cramFile/codecs/external.js +1 -0
package/esm/cramFile/codecs/external.js.map +1 -1
package/esm/cramFile/codecs/gamma.js.map +1 -1
package/esm/cramFile/codecs/getBits.js.map +1 -1
package/esm/cramFile/codecs/huffman.d.ts +0 -1
package/esm/cramFile/codecs/huffman.js +1 -3
package/esm/cramFile/codecs/huffman.js.map +1 -1
package/esm/cramFile/codecs/index.js.map +1 -1
package/esm/cramFile/codecs/subexp.js.map +1 -1
package/esm/cramFile/container/compressionScheme.js +1 -1
package/esm/cramFile/container/compressionScheme.js.map +1 -1
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/encoding.d.ts +20 -20
package/esm/cramFile/file.d.ts +14 -7
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/filehandle.d.ts +1 -2
package/esm/cramFile/index.d.ts +1 -2
package/esm/cramFile/index.js +1 -2
package/esm/cramFile/index.js.map +1 -1
package/esm/cramFile/record.d.ts +6 -6
package/esm/cramFile/record.js +7 -4
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/sectionParsers.d.ts +9 -8
package/esm/cramFile/sectionParsers.js +10 -11
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.js +7 -11
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/slice/index.js +24 -22
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.d.ts +1 -0
package/esm/cramFile/util.js +1 -1
package/esm/cramFile/util.js.map +1 -1
package/esm/index.d.ts +3 -4
package/esm/index.js +3 -4
package/esm/index.js.map +1 -1
package/esm/indexedCramFile.d.ts +6 -6
package/esm/indexedCramFile.js +13 -18
package/esm/indexedCramFile.js.map +1 -1
package/esm/io/index.d.ts +2 -1
package/esm/io/index.js +2 -1
package/esm/io/index.js.map +1 -1
package/esm/rans/d04.js.map +1 -1
package/esm/rans/d14.js.map +1 -1
package/esm/rans/decoding.js.map +1 -1
package/esm/rans/frequencies.js.map +1 -1
package/esm/rans/index.js.map +1 -1
package/esm/sam.d.ts +5 -6
package/esm/sam.js +20 -7
package/esm/sam.js.map +1 -1
package/esm/typescript.js.map +1 -1
package/esm/unzip.d.ts +2 -2
package/esm/unzip.js +1 -2
package/esm/unzip.js.map +1 -1
package/package.json +11 -11
package/src/craiIndex.ts +8 -13
package/src/cramFile/codecs/_base.ts +3 -3
package/src/cramFile/codecs/external.ts +1 -0
package/src/cramFile/codecs/huffman.ts +7 -8
package/src/cramFile/container/compressionScheme.ts +1 -1
package/src/cramFile/encoding.ts +10 -10
package/src/cramFile/file.ts +5 -5
package/src/cramFile/filehandle.ts +1 -3
package/src/cramFile/index.ts +1 -2
package/src/cramFile/record.ts +13 -10
package/src/cramFile/sectionParsers.ts +8 -9
package/src/cramFile/slice/decodeRecord.ts +15 -17
package/src/cramFile/slice/index.ts +26 -23
package/src/cramFile/util.ts +1 -1
package/src/index.ts +3 -5
package/src/indexedCramFile.ts +19 -23
package/src/io/index.ts +3 -1
package/src/sam.ts +28 -14
package/src/typings/binary-parser.d.ts +1 -1
package/src/unzip.ts +1 -2

package/esm/cramFile/codecs/subexp.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAKnC,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,SAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;~~YAC3B~~,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;~~SACF~~;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE;~~YAC3D~~,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;~~SACpC~~;QAED,IAAI,CAAC,CAAA;QACL,IAAI,CAAC,CAAA;QACL,IAAI,cAAc,KAAK,CAAC,EAAE;~~YACxB~~,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;~~SACzD~~;aAAM;~~YACL~~,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,IAAI,GAAG,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YACjE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;~~SACpB~~;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF"}
1	+ {"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAKnC,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,SAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC;YAC5D,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;QACrC,CAAC;QAED,IAAI,CAAC,CAAA;QACL,IAAI,CAAC,CAAA;QACL,IAAI,cAAc,KAAK,CAAC,EAAE,CAAC;YACzB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QAC1D,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,IAAI,GAAG,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YACjE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;QACrB,CAAC;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF"}

package/esm/cramFile/container/compressionScheme.js CHANGED Viewed

@@ -121,7 +121,7 @@ export default class CramContainerCompressionScheme {
     toJSON() {
         const data = {};
         Object.keys(this).forEach(k => {
-            if (/Cache$/.test(k)) {
+            if (k.endsWith('Cache')) {
                 return;
             }
             data[k] = this[k];

package/esm/cramFile/container/compressionScheme.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AAEjD,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAC1D,OAAO,SAAS,MAAM,UAAU,CAAA;AAChC,OAAO,8BAA8B,MAAM,qBAAqB,CAAA;AAGhE,MAAM,CAAC,OAAO,OAAO,aAAa;IAChC,YACS,IAAc,EACd,YAAoB;QADpB,SAAI,GAAJ,IAAI,CAAU;QACd,iBAAY,GAAZ,YAAY,CAAQ;IAC1B,CAAC;IAEJ,UAAU;IACV,SAAS;QACP,OAAO,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,KAAK,CAAC,yBAAyB;QAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAE9C,gFAAgF;QAChF,IAAI,CAAC,eAAe,CAAC,UAAU,EAAE,CAAC;YAChC,OAAO,IAAI,CAAA;QACb,CAAC;QACD,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,iBAAiB,EAAE,CAAA;QAC1D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACxC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,IAAI,KAAK,CAAC,WAAW,KAAK,oBAAoB,EAAE,CAAC;YAC/C,MAAM,IAAI,kBAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,yDAAyD,CACnG,CAAA;QACH,CAAC;QACD,MAAM,OAAO,GAAG,SAAS,CACvB,KAAK,CAAC,OAAO,EACb,cAAc,CAAC,qBAAqB,CAAC,MAAM,EAC3C,CAAC,EACD,KAAK,CAAC,eAAe,CACtB,CAAA;QACD,OAAO;YACL,GAAG,KAAK;YACR,aAAa,EAAE,OAAO;SACvB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED,kFAAkF;IAClF,UAAU;IACV,KAAK,CAAC,oBAAoB;QACxB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,yBAAyB,EAAE,CAAA;QACrD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,OAAO,IAAI,8BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;IACjE,CAAC;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,SAAS,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,CAAA;IACtD,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,QAAgB;QACzC,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,iBAAiB,EAAE,CAAA;QAC1D,MAAM,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QACrE,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QAEjD,IAAI,QAAQ,IAAI,QAAQ,EAAE,CAAC;YACzB,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,wEAAwE;QACxE,iDAAiD;QACjD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,oBAAoB,CAAC,SAAS,CAAC,CAAA;QACjE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,oBAAoB,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;QACzE,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAQ,CAAA;QACrE,MAAM,gBAAgB,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACvD,IAAI,QAAQ,GAAG,OAAO,CAAC,MAAM,IAAI,QAAQ,EAAE,CAAC;YAC1C,OAAO,CAAC,IAAI,CACV,GAAG,IAAI,CAAC,IAAI,yBAAyB,QAAQ,4CAA4C,OAAO,CAAC,MAAM,yEAAyE,CACjL,CAAA;YACD,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAC/B,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,CACrD,CAAA;QACD,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAClB,MAAM,EACN,CAAC,EACD,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,EACpD,QAAQ,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,CAC5C,CAAA;QACD,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAE9D,IAAI,IAAI,CAAC,IAAI,CAAC,iBAAiB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;YAC/D,MAAM,IAAI,CAAC,IAAI,CAAC,UAAU,CACxB,QAAQ,EACR,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,CAAC,EACpD,OAAO,CAAC,KAAK,EACb,0CAA0C,QAAQ,EAAE,CACrD,CAAA;QACH,CAAC;QAED,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE;YACrD,KAAK,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB;YACvD,YAAY,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,QAAQ;SAC1E,CAAC,CAAA;QAEF,OAAO,cAAc,CAAA;IACvB,CAAC;CACF;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,aAAa,EAAE,MAAM,CAAC,CAAC,CAAA"}

package/esm/cramFile/encoding.d.ts CHANGED Viewed

@@ -1,24 +1,24 @@
-export type NullEncoding = {
+export interface NullEncoding {
     codecId: 0;
     parametersBytes: number;
     parameters: Record<string, never>;
-};
-export type ExternalCramEncoding = {
+}
+export interface ExternalCramEncoding {
     codecId: 1;
     parametersBytes: number;
     parameters: {
         blockContentId: number;
     };
-};
-export type GolombEncoding = {
+}
+export interface GolombEncoding {
     codecId: 2;
     parametersBytes: number;
     parameters: {
         offset: number;
         M: number;
     };
-};
-export type HuffmanEncoding = {
+}
+export interface HuffmanEncoding {
     codecId: 3;
     parametersBytes: number;
     parameters: {
@@ -27,52 +27,52 @@ export type HuffmanEncoding = {
         numLengths: number;
         bitLengths: number[];
     };
-};
-export type ByteArrayLengthEncoding = {
+}
+export interface ByteArrayLengthEncoding {
     codecId: 4;
     parametersBytes: number;
     parameters: {
         lengthsEncoding: CramEncoding;
         valuesEncoding: CramEncoding;
     };
-};
-export type ByteArrayStopCramEncoding = {
+}
+export interface ByteArrayStopCramEncoding {
     codecId: 5;
     parametersBytes: number;
     parameters: {
         stopByte: number;
         blockContentId: number;
     };
-};
-export type BetaEncoding = {
+}
+export interface BetaEncoding {
     codecId: 6;
     parametersBytes: number;
     parameters: {
         offset: number;
         length: number;
     };
-};
-export type SubexpEncoding = {
+}
+export interface SubexpEncoding {
     codecId: 7;
     parametersBytes: number;
     parameters: {
         offset: number;
         K: number;
     };
-};
-export type GolombRiceEncoding = {
+}
+export interface GolombRiceEncoding {
     codecId: 8;
     parametersBytes: number;
     parameters: {
         offset: number;
         log2m: number;
     };
-};
-export type GammaEncoding = {
+}
+export interface GammaEncoding {
     codecId: 9;
     parametersBytes: number;
     parameters: {
         offset: number;
     };
-};
+}
 export type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;

package/esm/cramFile/file.d.ts CHANGED Viewed

@@ -1,3 +1,4 @@
+/// <reference path="../../src/typings/binary-parser.d.ts" />
 /// <reference types="node" />
 import QuickLRU from 'quick-lru';
 import { Parser } from '@gmod/binary-parser';
@@ -5,16 +6,16 @@ import { BlockHeader, CompressionMethod } from './sectionParsers';
 import CramContainer from './container';
 import CramRecord from './record';
 import { Filehandle } from './filehandle';
-export type CramFileSource = {
+export interface CramFileSource {
     filehandle?: Filehandle;
     url?: string;
     path?: string;
-};
+}
 export type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
 export type CramFileArgs = CramFileSource & {
-    checkSequenceMD5: boolean;
+    checkSequenceMD5?: boolean;
     cacheSize?: number;
-    seqFetch: SeqFetch;
+    seqFetch?: SeqFetch;
 };
 export type CramFileBlock = BlockHeader & {
     _endPosition: number;
@@ -26,9 +27,9 @@ export type CramFileBlock = BlockHeader & {
 export default class CramFile {
     private file;
     validateChecksums: boolean;
-    fetchReferenceSequenceCallback: SeqFetch;
+    fetchReferenceSequenceCallback?: SeqFetch;
     options: {
-        checkSequenceMD5: boolean;
+        checkSequenceMD5?: boolean;
         cacheSize: number;
     };
     featureCache: QuickLRU<string, Promise<CramRecord[]>>;
@@ -40,7 +41,13 @@ export default class CramFile {
     }>;
     stat(): Promise<import("generic-filehandle").Stats>;
     getDefinition(): Promise<any>;
-    getSamHeader(): Promise<import("../sam").HeaderDataItem[]>;
+    getSamHeader(): Promise<{
+        tag: string;
+        data: {
+            tag: string;
+            value: string | undefined;
+        }[];
+    }[]>;
     getHeaderText(): Promise<string | undefined>;
     getSectionParsers(): Promise<{
         cramFileDefinition: {

package/esm/cramFile/file.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/cramFile/filehandle.d.ts CHANGED Viewed

@@ -1,2 +1 @@
-import { GenericFilehandle } from 'generic-filehandle';
-export { GenericFilehandle as Filehandle };
+export { GenericFilehandle as Filehandle } from 'generic-filehandle';

package/esm/cramFile/index.d.ts CHANGED Viewed

@@ -1,3 +1,2 @@
-import CramFile from './file';
 export { default as CramRecord } from './record';
-export default CramFile;
+export { default } from './file';

package/esm/cramFile/index.js CHANGED Viewed

@@ -1,4 +1,3 @@
-import CramFile from './file';
 export { default as CramRecord } from './record';
-export default CramFile;
+export { default } from './file';
 //# sourceMappingURL=index.js.map

package/esm/cramFile/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,UAAU,CAAA;AAEhD,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA"}

package/esm/cramFile/record.d.ts CHANGED Viewed

@@ -1,25 +1,25 @@
 import CramContainerCompressionScheme from './container/compressionScheme';
 import decodeRecord from './slice/decodeRecord';
-export type RefRegion = {
+export interface RefRegion {
     start: number;
     end: number;
     seq: string;
-};
-export type ReadFeature = {
+}
+export interface ReadFeature {
     code: string;
     pos: number;
     refPos: number;
     data: any;
     ref?: string;
     sub?: string;
-};
-export type MateRecord = {
+}
+export interface MateRecord {
     readName?: string;
     sequenceId: number;
     alignmentStart: number;
     flags?: number;
     uniqueId?: number;
-};
+}
 export declare const BamFlags: readonly [readonly [1, "Paired"], readonly [2, "ProperlyPaired"], readonly [4, "SegmentUnmapped"], readonly [8, "MateUnmapped"], readonly [16, "ReverseComplemented"], readonly [32, "MateReverseComplemented"], readonly [64, "Read1"], readonly [128, "Read2"], readonly [256, "Secondary"], readonly [512, "FailedQc"], readonly [1024, "Duplicate"], readonly [2048, "Supplementary"]];
 export declare const CramFlags: readonly [readonly [1, "PreservingQualityScores"], readonly [2, "Detached"], readonly [4, "WithMateDownstream"], readonly [8, "DecodeSequenceAsStar"]];
 export declare const MateFlags: readonly [readonly [1, "OnNegativeStrand"], readonly [2, "Unmapped"]];

package/esm/cramFile/record.js CHANGED Viewed

@@ -11,7 +11,7 @@ function decodeReadSequence(cramRecord, refRegion) {
     const regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
     if (!cramRecord.readFeatures) {
         return refRegion.seq
-            .substr(regionSeqOffset, cramRecord.lengthOnRef)
+            .slice(regionSeqOffset, regionSeqOffset + (cramRecord.lengthOnRef || 0))
             .toUpperCase();
     }
     let bases = '';
@@ -75,14 +75,17 @@ function decodeReadSequence(cramRecord, refRegion) {
             }
             else if (currentReadFeature < cramRecord.readFeatures.length) {
                 // put down a chunk of sequence up to the next read feature
-                const chunk = refRegion.seq.substr(regionPos, cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1);
+                const chunk = refRegion.seq.slice(regionPos, regionPos +
+                    cramRecord.readFeatures[currentReadFeature].pos -
+                    bases.length -
+                    1);
                 bases += chunk;
                 regionPos += chunk.length;
             }
         }
         else {
             // put down a chunk of reference up to the full read length
-            const chunk = refRegion.seq.substr(regionPos, cramRecord.readLength - bases.length);
+            const chunk = refRegion.seq.slice(regionPos, regionPos + cramRecord.readLength - bases.length);
             bases += chunk;
             regionPos += chunk.length;
         }
@@ -362,7 +365,7 @@ export default class CramRecord {
     toJSON() {
         const data = {};
         Object.keys(this).forEach(k => {
-            if (k.charAt(0) === '_') {
+            if (k.startsWith('_')) {
                 return;
             }
             data[k] = this[k];

package/esm/cramFile/record.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/cramFile/sectionParsers.d.ts CHANGED Viewed

@@ -1,3 +1,4 @@
+/// <reference path="../../src/typings/binary-parser.d.ts" />
 import { Parser } from '@gmod/binary-parser';
 import { TupleOf } from '../typescript';
 import { ParsedItem } from './util';
@@ -8,7 +9,7 @@ declare const cramFileDefinition: {
     maxLength: number;
 };
 export type CramTagDictionary = string[][];
-export type CramPreservationMap = {
+export interface CramPreservationMap {
     MI: boolean;
     UI: boolean;
     PI: boolean;
@@ -17,8 +18,8 @@ export type CramPreservationMap = {
     RR: boolean;
     SM: [number, number, number, number, number];
     TD: CramTagDictionary;
-};
-export type MappedSliceHeader = {
+}
+export interface MappedSliceHeader {
     refSeqId: number;
     refSeqStart: number;
     refSeqSpan: number;
@@ -29,24 +30,24 @@ export type MappedSliceHeader = {
     contentIds: number[];
     refBaseBlockId: number;
     md5: TupleOf<number, 16>;
-};
-export type UnmappedSliceHeader = {
+}
+export interface UnmappedSliceHeader {
     numRecords: number;
     recordCounter: number;
     numBlocks: number;
     numContentIds: number;
     contentIds: number[];
     md5: TupleOf<number, 16>;
-};
+}
 export declare function isMappedSliceHeader(header: MappedSliceHeader | UnmappedSliceHeader): header is MappedSliceHeader;
 export type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
-export type BlockHeader = {
+export interface BlockHeader {
     compressionMethod: CompressionMethod;
     contentType: 'FILE_HEADER' | 'COMPRESSION_HEADER' | 'MAPPED_SLICE_HEADER' | 'UNMAPPED_SLICE_HEADER' | 'EXTERNAL_DATA' | 'CORE_DATA';
     contentId: number;
     compressedSize: number;
     uncompressedSize: number;
-};
+}
 export type CramCompressionHeader = ParsedItem<{
     preservation: CramPreservationMap;
     dataSeriesEncoding: DataSeriesEncodingMap;

package/esm/cramFile/sectionParsers.js CHANGED Viewed

@@ -35,7 +35,7 @@ const cramBlockHeader = {
                 'FILE_HEADER',
                 'COMPRESSION_HEADER',
                 'MAPPED_SLICE_HEADER',
-                'UNMAPPED_SLICE_HEADER',
+                'UNMAPPED_SLICE_HEADER', // < only used in cram v1
                 'EXTERNAL_DATA',
                 'CORE_DATA',
             ][b];
@@ -61,7 +61,7 @@ const cramTagDictionary = new Parser().itf8('size').buffer('ents', {
             const str = buffer.toString('utf8', stringStart, stringEnd);
             const tags = [];
             for (let i = 0; i < str.length; i += 3) {
-                tags.push(str.substr(i, 3));
+                tags.push(str.slice(i, i + 3));
             }
             return tags;
         }
@@ -117,8 +117,7 @@ const cramPreservationMap = new Parser()
 /* istanbul ignore next */
 function formatMap(data) {
     const map = {};
-    for (let i = 0; i < data.ents.length; i += 1) {
-        const { key, value } = data.ents[i];
+    for (const { key, value } of data.ents) {
         if (map[key]) {
             console.warn(`duplicate key ${key} in map`);
         }
@@ -201,7 +200,7 @@ const versionedParsers = {
         const maxLengthFunc = (numContentIds) => maxLength + numContentIds * 5;
         return { parser, maxLength: maxLengthFunc };
     },
-    cramEncoding(majorVersion) {
+    cramEncoding(_majorVersion) {
         const parser = new Parser()
             .namely('cramEncoding')
             .itf8('codecId')
@@ -209,9 +208,9 @@ const versionedParsers = {
             .choice('parameters', {
             tag: 'codecId',
             choices: {
-                0: new Parser(),
-                1: new Parser().itf8('blockContentId'),
-                2: new Parser().itf8('offset').itf8('M'),
+                0: new Parser(), // NULL
+                1: new Parser().itf8('blockContentId'), // EXTERNAL
+                2: new Parser().itf8('offset').itf8('M'), // GOLOMB,
                 // HUFFMAN_INT
                 3: Parser.start()
                     .itf8('numCodes')
@@ -223,9 +222,9 @@ const versionedParsers = {
                     .nest('valuesEncoding', { type: 'cramEncoding' }),
                 // BYTE_ARRAY_STOP is a little different for CRAM v1
                 5: new Parser().uint8('stopByte').itf8('blockContentId'),
-                6: new Parser().itf8('offset').itf8('length'),
-                7: new Parser().itf8('offset').itf8('K'),
-                8: new Parser().itf8('offset').itf8('log2m'),
+                6: new Parser().itf8('offset').itf8('length'), // BETA
+                7: new Parser().itf8('offset').itf8('K'), // SUBEXP
+                8: new Parser().itf8('offset').itf8('log2m'), // GOLOMB_RICE
                 9: new Parser().itf8('offset'), // GAMMA
             },
         });

package/esm/cramFile/sectionParsers.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/esm/cramFile/slice/decodeRecord.js CHANGED Viewed

@@ -135,7 +135,7 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
         // map of operator name -> data series name
         const data1Schema = {
             B: ['character', 'BA'],
-            S: ['string', majorVersion > 1 ? 'SC' : 'IN'],
+            S: ['string', majorVersion > 1 ? 'SC' : 'IN'], // IN if cram v1, SC otherwise
             X: ['number', 'BS'],
             D: ['number', 'DL'],
             I: ['string', 'IN'],
@@ -181,15 +181,11 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
     // in javascript land.
     const cramFlags = decodeDataSeries('CF');
     if (!isMappedSliceHeader(sliceHeader.parsedContent)) {
-        throw new Error();
-    }
-    let sequenceId;
-    if (majorVersion > 1 && sliceHeader.parsedContent.refSeqId === -2) {
-        sequenceId = decodeDataSeries('RI');
-    }
-    else {
-        sequenceId = sliceHeader.parsedContent.refSeqId;
+        throw new Error('slice header not mapped');
     }
+    const sequenceId = majorVersion > 1 && sliceHeader.parsedContent.refSeqId === -2
+        ? decodeDataSeries('RI')
+        : sliceHeader.parsedContent.refSeqId;
     const readLength = decodeDataSeries('RL');
     // if APDelta, will calculate the true start in a second pass
     let alignmentStart = decodeDataSeries('AP');
@@ -252,8 +248,8 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
     const ntags = TN.length;
     for (let i = 0; i < ntags; i += 1) {
         const tagId = TN[i];
-        const tagName = tagId.substr(0, 2);
-        const tagType = tagId.substr(2, 1);
+        const tagName = tagId.slice(0, 2);
+        const tagType = tagId.slice(2, 3);
         const tagCodec = compressionScheme.getCodecForTag(tagId);
         if (!tagCodec) {
             throw new CramMalformedError(`no codec defined for auxiliary tag ${tagId}`);