@gmod/bam 7.1.3 → 7.1.5

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 (16) hide show
  1. package/CHANGELOG.md +4 -6
  2. package/dist/cigar.d.ts +9 -0
  3. package/dist/cigar.js +13 -0
  4. package/dist/cigar.js.map +1 -0
  5. package/dist/record.d.ts +12 -20
  6. package/dist/record.js +148 -163
  7. package/dist/record.js.map +1 -1
  8. package/esm/cigar.d.ts +9 -0
  9. package/esm/cigar.js +10 -0
  10. package/esm/cigar.js.map +1 -0
  11. package/esm/record.d.ts +12 -20
  12. package/esm/record.js +145 -160
  13. package/esm/record.js.map +1 -1
  14. package/package.json +1 -1
  15. package/src/cigar.ts +9 -0
  16. package/src/record.ts +170 -201
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/cigar.d.ts ADDED
@@ -0,0 +1,9 @@
1
+ export declare const CIGAR_MATCH = 0;
2
+ export declare const CIGAR_INS = 1;
3
+ export declare const CIGAR_DEL = 2;
4
+ export declare const CIGAR_REF_SKIP = 3;
5
+ export declare const CIGAR_SOFT_CLIP = 4;
6
+ export declare const CIGAR_HARD_CLIP = 5;
7
+ export declare const CIGAR_PAD = 6;
8
+ export declare const CIGAR_EQUAL = 7;
9
+ export declare const CIGAR_DIFF = 8;
package/esm/cigar.js ADDED
@@ -0,0 +1,10 @@
1
+ export const CIGAR_MATCH = 0;
2
+ export const CIGAR_INS = 1;
3
+ export const CIGAR_DEL = 2;
4
+ export const CIGAR_REF_SKIP = 3;
5
+ export const CIGAR_SOFT_CLIP = 4;
6
+ export const CIGAR_HARD_CLIP = 5;
7
+ export const CIGAR_PAD = 6;
8
+ export const CIGAR_EQUAL = 7;
9
+ export const CIGAR_DIFF = 8;
10
+ //# sourceMappingURL=cigar.js.map
package/esm/cigar.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"cigar.js","sourceRoot":"","sources":["../src/cigar.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,WAAW,GAAG,CAAC,CAAA;AAC5B,MAAM,CAAC,MAAM,SAAS,GAAG,CAAC,CAAA;AAC1B,MAAM,CAAC,MAAM,SAAS,GAAG,CAAC,CAAA;AAC1B,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAA;AAC/B,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC,CAAA;AAChC,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC,CAAA;AAChC,MAAM,CAAC,MAAM,SAAS,GAAG,CAAC,CAAA;AAC1B,MAAM,CAAC,MAAM,WAAW,GAAG,CAAC,CAAA;AAC5B,MAAM,CAAC,MAAM,UAAU,GAAG,CAAC,CAAA"}
package/esm/record.d.ts CHANGED
@@ -3,10 +3,18 @@ interface Bytes {
3
3
  end: number;
4
4
  byteArray: Uint8Array;
5
5
  }
6
+ interface CIGAR_AND_LENGTH {
7
+ length_on_ref: number;
8
+ NUMERIC_CIGAR: Uint32Array;
9
+ }
6
10
  export default class BamRecord {
7
11
  fileOffset: number;
8
12
  private bytes;
9
13
  private _dataView;
14
+ private _cachedFlags?;
15
+ private _cachedTags?;
16
+ private _cachedCigarAndLength?;
17
+ private _cachedNUMERIC_MD?;
10
18
  constructor(args: {
11
19
  bytes: Bytes;
12
20
  fileOffset: number;
@@ -19,43 +27,27 @@ export default class BamRecord {
19
27
  get id(): number;
20
28
  get mq(): number | undefined;
21
29
  get score(): number | undefined;
22
- get qual(): Uint8Array<ArrayBufferLike> | undefined;
30
+ get qual(): Uint8Array<ArrayBufferLike> | null;
23
31
  get strand(): 1 | -1;
24
32
  get b0(): number;
25
33
  get name(): string;
26
34
  get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
27
35
  get tags(): Record<string, unknown>;
28
- /**
29
- * @returns {boolean} true if the read is paired, regardless of whether both
30
- * segments are mapped
31
- */
36
+ private _computeTags;
32
37
  isPaired(): boolean;
33
- /** @returns {boolean} true if the read is paired, and both segments are mapped */
34
38
  isProperlyPaired(): boolean;
35
- /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
36
39
  isSegmentUnmapped(): boolean;
37
- /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
38
40
  isMateUnmapped(): boolean;
39
- /** @returns {boolean} true if the read is mapped to the reverse strand */
40
41
  isReverseComplemented(): boolean;
41
- /** @returns {boolean} true if the mate is mapped to the reverse strand */
42
42
  isMateReverseComplemented(): boolean;
43
- /** @returns {boolean} true if this is read number 1 in a pair */
44
43
  isRead1(): boolean;
45
- /** @returns {boolean} true if this is read number 2 in a pair */
46
44
  isRead2(): boolean;
47
- /** @returns {boolean} true if this is a secondary alignment */
48
45
  isSecondary(): boolean;
49
- /** @returns {boolean} true if this read has failed QC checks */
50
46
  isFailedQc(): boolean;
51
- /** @returns {boolean} true if the read is an optical or PCR duplicate */
52
47
  isDuplicate(): boolean;
53
- /** @returns {boolean} true if this is a supplementary alignment */
54
48
  isSupplementary(): boolean;
55
- get cigarAndLength(): {
56
- NUMERIC_CIGAR: Uint32Array<ArrayBufferLike>;
57
- length_on_ref: number;
58
- };
49
+ get cigarAndLength(): CIGAR_AND_LENGTH;
50
+ private _computeCigarAndLength;
59
51
  get length_on_ref(): number;
60
52
  get NUMERIC_CIGAR(): Uint32Array<ArrayBufferLike>;
61
53
  get CIGAR(): string;