@gmod/bam 3.0.2 → 4.0.0

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Files changed (14) hide show
  1. package/CHANGELOG.md +8 -0
  2. package/dist/bai.js +1 -1
  3. package/dist/bai.js.map +1 -1
  4. package/dist/record.d.ts +1 -2
  5. package/dist/record.js +128 -151
  6. package/dist/record.js.map +1 -1
  7. package/esm/bai.js +1 -1
  8. package/esm/bai.js.map +1 -1
  9. package/esm/record.d.ts +1 -2
  10. package/esm/record.js +128 -151
  11. package/esm/record.js.map +1 -1
  12. package/package.json +1 -1
  13. package/src/bai.ts +2 -1
  14. package/src/record.ts +112 -152
package/esm/record.js CHANGED
@@ -32,10 +32,6 @@ export default class BamRecord {
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  return this.mq;
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  }
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  get qual() {
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- var _a;
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- return (_a = this.qualRaw) === null || _a === void 0 ? void 0 : _a.join(' ');
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- }
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- get qualRaw() {
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  if (this.isSegmentUnmapped()) {
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  return;
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  }
@@ -67,162 +63,143 @@ export default class BamRecord {
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  const tag = String.fromCharCode(byteArray[p], byteArray[p + 1]);
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  const type = String.fromCharCode(byteArray[p + 2]);
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  p += 3;
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- let value;
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- switch (type) {
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- case 'A': {
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- value = String.fromCharCode(byteArray[p]);
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- p += 1;
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- break;
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- }
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- case 'i': {
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- value = byteArray.readInt32LE(p);
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- p += 4;
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- break;
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- }
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- case 'I': {
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- value = byteArray.readUInt32LE(p);
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- p += 4;
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- break;
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- }
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- case 'c': {
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- value = byteArray.readInt8(p);
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- p += 1;
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- break;
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- }
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- case 'C': {
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- value = byteArray.readUInt8(p);
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- p += 1;
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- break;
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- }
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- case 's': {
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- value = byteArray.readInt16LE(p);
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- p += 2;
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- break;
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- }
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- case 'S': {
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- value = byteArray.readUInt16LE(p);
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- p += 2;
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- break;
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- }
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- case 'f': {
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- value = byteArray.readFloatLE(p);
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- p += 4;
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- break;
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- }
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- case 'Z':
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- case 'H': {
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- value = '';
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- while (p <= blockEnd) {
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- const cc = byteArray[p++];
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- if (cc === 0) {
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- break;
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- }
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- else {
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- value += String.fromCharCode(cc);
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- }
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- }
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- break;
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- }
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- case 'B': {
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- value = '';
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+ if (type === 'A') {
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+ tags[tag] = String.fromCharCode(byteArray[p]);
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+ p += 1;
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+ }
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+ else if (type === 'i') {
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+ tags[tag] = byteArray.readInt32LE(p);
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+ p += 4;
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+ }
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+ else if (type === 'I') {
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+ tags[tag] = byteArray.readUInt32LE(p);
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+ p += 4;
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+ }
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+ else if (type === 'c') {
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+ tags[tag] = byteArray.readInt8(p);
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+ p += 1;
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+ }
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+ else if (type === 'C') {
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+ tags[tag] = byteArray.readUInt8(p);
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+ p += 1;
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+ }
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+ else if (type === 's') {
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+ tags[tag] = byteArray.readInt16LE(p);
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+ p += 2;
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+ }
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+ else if (type === 'S') {
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+ tags[tag] = byteArray.readUInt16LE(p);
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+ p += 2;
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+ }
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+ else if (type === 'f') {
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+ tags[tag] = byteArray.readFloatLE(p);
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+ p += 4;
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+ }
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+ else if (type === 'Z' || type === 'H') {
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+ const value = [];
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+ while (p <= blockEnd) {
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  const cc = byteArray[p++];
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- const Btype = String.fromCharCode(cc);
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- const limit = byteArray.readInt32LE(p);
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- p += 4;
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- if (Btype === 'i') {
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- if (tag === 'CG') {
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- for (let k = 0; k < limit; k++) {
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- const cigop = byteArray.readInt32LE(p);
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- const lop = cigop >> 4;
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- const op = CIGAR_DECODER[cigop & 0xf];
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- value += lop + op;
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- p += 4;
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- }
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- }
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- else {
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- for (let k = 0; k < limit; k++) {
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- value += byteArray.readInt32LE(p);
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- if (k + 1 < limit) {
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- value += ',';
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- }
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- p += 4;
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- }
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- }
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+ if (cc !== 0) {
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+ value.push(String.fromCharCode(cc));
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  }
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- if (Btype === 'I') {
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- if (tag === 'CG') {
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- for (let k = 0; k < limit; k++) {
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- const cigop = byteArray.readUInt32LE(p);
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- const lop = cigop >> 4;
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- const op = CIGAR_DECODER[cigop & 0xf];
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- value += lop + op;
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- p += 4;
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- }
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- }
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- else {
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- for (let k = 0; k < limit; k++) {
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- value += byteArray.readUInt32LE(p);
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- if (k + 1 < limit) {
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- value += ',';
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- }
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- p += 4;
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- }
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- }
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+ else {
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+ break;
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  }
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- if (Btype === 's') {
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- for (let k = 0; k < limit; k++) {
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- value += byteArray.readInt16LE(p);
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- if (k + 1 < limit) {
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- value += ',';
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- }
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- p += 2;
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- }
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- }
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- if (Btype === 'S') {
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+ }
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+ tags[tag] = value.join('');
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+ }
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+ else if (type === 'B') {
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+ const cc = byteArray[p++];
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+ const Btype = String.fromCharCode(cc);
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+ const limit = byteArray.readInt32LE(p);
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+ p += 4;
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+ if (Btype === 'i') {
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+ if (tag === 'CG') {
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+ const value = [];
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  for (let k = 0; k < limit; k++) {
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- value += byteArray.readUInt16LE(p);
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- if (k + 1 < limit) {
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- value += ',';
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- }
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- p += 2;
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+ const cigop = byteArray.readInt32LE(p);
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+ const lop = cigop >> 4;
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+ const op = CIGAR_DECODER[cigop & 0xf];
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+ value.push(lop + op);
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+ p += 4;
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  }
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+ tags[tag] = value.join('');
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  }
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- if (Btype === 'c') {
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+ else {
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+ const value = [];
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  for (let k = 0; k < limit; k++) {
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- value += byteArray.readInt8(p);
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- if (k + 1 < limit) {
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- value += ',';
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- }
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- p += 1;
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+ value.push(byteArray.readInt32LE(p));
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+ p += 4;
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  }
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+ tags[tag] = value;
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  }
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- if (Btype === 'C') {
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+ }
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+ else if (Btype === 'I') {
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+ if (tag === 'CG') {
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+ const value = [];
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  for (let k = 0; k < limit; k++) {
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- value += byteArray.readUInt8(p);
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- if (k + 1 < limit) {
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- value += ',';
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- }
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- p += 1;
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+ const cigop = byteArray.readUInt32LE(p);
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+ const lop = cigop >> 4;
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+ const op = CIGAR_DECODER[cigop & 0xf];
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+ value.push(lop + op);
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+ p += 4;
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  }
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+ tags[tag] = value.join('');
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  }
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- if (Btype === 'f') {
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+ else {
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+ const value = [];
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  for (let k = 0; k < limit; k++) {
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- value += byteArray.readFloatLE(p);
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- if (k + 1 < limit) {
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- value += ',';
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- }
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+ value.push(byteArray.readUInt32LE(p));
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  p += 4;
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  }
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+ tags[tag] = value;
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  }
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- break;
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  }
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- default: {
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- console.warn(`Unknown BAM tag type '${type}', tags may be incomplete`);
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- value = undefined;
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- p = blockEnd;
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- } // stop parsing tags
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+ else if (Btype === 's') {
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+ const value = [];
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+ for (let k = 0; k < limit; k++) {
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+ value.push(byteArray.readInt16LE(p));
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+ p += 2;
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+ }
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+ tags[tag] = value;
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+ }
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+ else if (Btype === 'S') {
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+ const value = [];
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+ for (let k = 0; k < limit; k++) {
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+ value.push(byteArray.readUInt16LE(p));
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+ p += 2;
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+ }
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+ tags[tag] = value;
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+ }
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+ else if (Btype === 'c') {
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+ const value = [];
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+ for (let k = 0; k < limit; k++) {
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+ value.push(byteArray.readInt8(p));
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+ p += 1;
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+ }
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+ tags[tag] = value;
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+ }
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+ else if (Btype === 'C') {
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+ const value = [];
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+ for (let k = 0; k < limit; k++) {
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+ value.push(byteArray.readUInt8(p));
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+ p += 1;
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+ }
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+ tags[tag] = value;
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+ }
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+ else if (Btype === 'f') {
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+ const value = [];
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+ for (let k = 0; k < limit; k++) {
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+ value.push(byteArray.readFloatLE(p));
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+ p += 4;
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+ }
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+ tags[tag] = value;
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+ }
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+ }
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+ else {
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+ console.error('Unknown BAM tag type', type);
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+ break;
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  }
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- tags[tag] = value;
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  }
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  return tags;
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  }
@@ -286,7 +263,7 @@ export default class BamRecord {
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  }
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  const numCigarOps = this.num_cigar_ops;
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  let p = this.b0 + this.read_name_length;
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- let CIGAR = '';
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+ const CIGAR = [];
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  // check for CG tag by inspecting whether the CIGAR field contains a clip
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  // that consumes entire seqLen
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  let cigop = this.byteArray.readInt32LE(p);
@@ -313,16 +290,16 @@ export default class BamRecord {
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  cigop = this.byteArray.readInt32LE(p);
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  lop = cigop >> 4;
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  op = CIGAR_DECODER[cigop & 0xf];
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- CIGAR += lop + op;
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- // soft clip, hard clip, and insertion don't count toward
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- // the length on the reference
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+ CIGAR.push(lop + op);
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+ // soft clip, hard clip, and insertion don't count toward the length on
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+ // the reference
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  if (op !== 'H' && op !== 'S' && op !== 'I') {
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  lref += lop;
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  }
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  p += 4;
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  }
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  return {
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- CIGAR,
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+ CIGAR: CIGAR.join(''),
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  length_on_ref: lref,
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  };
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  }
@@ -347,18 +324,18 @@ export default class BamRecord {
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  const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4;
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  const seqBytes = this.num_seq_bytes;
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  const len = this.seq_length;
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- let buf = '';
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+ const buf = [];
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  let i = 0;
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  for (let j = 0; j < seqBytes; ++j) {
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  const sb = byteArray[p + j];
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- buf += SEQRET_DECODER[(sb & 0xf0) >> 4];
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+ buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
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  i++;
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  if (i < len) {
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- buf += SEQRET_DECODER[sb & 0x0f];
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+ buf.push(SEQRET_DECODER[sb & 0x0f]);
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  i++;
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  }
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  }
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- return buf;
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+ return buf.join('');
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  }
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  // adapted from igv.js
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  get pair_orientation() {
package/esm/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "3.0.2",
3
+ "version": "4.0.0",
4
4
  "description": "Parser for BAM and BAM index (bai) files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bam-js",
package/src/bai.ts CHANGED
@@ -189,7 +189,7 @@ export default class BAI extends IndexFile {
189
189
  if (ba.binIndex[bin]) {
190
190
  const binChunks = ba.binIndex[bin]
191
191
  for (const binChunk of binChunks) {
192
- chunks.push(binChunk)
192
+ chunks.push(new Chunk(binChunk.minv, binChunk.maxv, bin))
193
193
  }
194
194
  }
195
195
  }
@@ -203,6 +203,7 @@ export default class BAI extends IndexFile {
203
203
  const maxLin = Math.min(max >> 14, nintv - 1)
204
204
  for (let i = minLin; i <= maxLin; ++i) {
205
205
  const vp = ba.linearIndex[i]
206
+
206
207
  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
207
208
  if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
208
209
  lowest = vp