clustal-js 2.0.8 → 2.0.10
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/pairwise.js +13 -2
- package/dist/pairwise.js.map +1 -1
- package/esm/pairwise.js +13 -2
- package/esm/pairwise.js.map +1 -1
- package/package.json +1 -1
- package/src/pairwise.ts +13 -2
package/dist/pairwise.js
CHANGED
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@@ -4,9 +4,17 @@ exports.getSeqBounds = getSeqBounds;
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4
4
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exports.parsePairwiseBlock = parsePairwiseBlock;
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exports.parsePairwiseBlocks = parsePairwiseBlocks;
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6
6
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const util_ts_1 = require("./util.js");
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7
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+
function isRulerLine(line) {
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8
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const trimmed = line.trim();
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9
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if (!trimmed) {
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10
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return false;
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11
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+
}
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12
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const fields = trimmed.split(/\s+/);
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return fields.every(f => /^\d+$/.test(f));
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}
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function isSequenceLine(line) {
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const trimmed = line.trim();
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9
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-
return /^\w+\s+/.test(trimmed);
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return /^\w+\s+/.test(trimmed) && !isRulerLine(line);
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10
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}
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function hasPositionNumbers(fields) {
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return fields.length >= 3 && /^\d+$/.test(fields[1]);
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@@ -27,7 +35,10 @@ function parsePairwiseBlock(arr) {
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return undefined;
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}
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while (line) {
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-
if (
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38
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+
if (isRulerLine(line)) {
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39
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// skip position ruler lines
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40
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+
}
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41
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+
else if (isSequenceLine(line)) {
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block.push(line);
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}
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else {
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package/dist/pairwise.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"pairwise.js","sourceRoot":"","sources":["../src/pairwise.ts"],"names":[],"mappings":";;
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1
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+
{"version":3,"file":"pairwise.js","sourceRoot":"","sources":["../src/pairwise.ts"],"names":[],"mappings":";;AAoBA,oCAMC;AAGD,gDAoCC;AAED,kDAYC;AA/ED,uCAAgD;AAEhD,SAAS,WAAW,CAAC,IAAY;IAC/B,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,OAAO,KAAK,CAAA;IACd,CAAC;IACD,MAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IACnC,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;AAC3C,CAAC;AAED,SAAS,cAAc,CAAC,IAAY;IAClC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,OAAO,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;AACtD,CAAC;AAED,SAAS,kBAAkB,CAAC,MAAgB;IAC1C,OAAO,MAAM,CAAC,MAAM,IAAI,CAAC,IAAI,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;AACtD,CAAC;AAED,SAAgB,YAAY,CAAC,IAAY,EAAE,QAAgB;IACzD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IACnC,MAAM,GAAG,GAAG,MAAM,CAAC,QAAQ,CAAC,CAAA;IAC5B,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAA;IAC9E,OAAO,CAAC,QAAQ,EAAE,QAAQ,GAAG,GAAG,CAAC,MAAM,CAAU,CAAA;AACnD,CAAC;AAED,sDAAsD;AACtD,SAAgB,kBAAkB,CAAC,GAAqB;IACtD,IAAI,IAAI,GAAG,IAAA,8BAAoB,EAAC,GAAG,CAAC,CAAA;IACpC,MAAM,KAAK,GAAa,EAAE,CAAA;IAC1B,IAAI,aAAa,GAAG,EAAE,CAAA;IACtB,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,OAAO,IAAI,EAAE,CAAC;QACZ,IAAI,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC;YACtB,4BAA4B;QAC9B,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,CAAC;YACN,aAAa,GAAG,IAAI,CAAA;QACtB,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;IACzB,CAAC;IAED,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAA;IACpD,MAAM,QAAQ,GAAG,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACtD,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;IACrD,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAA;IACzC,IAAI,SAAS,GAAG,aAAa,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAE/C,0DAA0D;IAC1D,MAAM,SAAS,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;IACnD,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;QAClB,SAAS,IAAI,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,CAAA;IACpC,CAAC;IACD,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,SAAS,EAAE,CAAA;AACjC,CAAC;AAED,SAAgB,mBAAmB,CAAC,GAAqB;IACvD,IAAI,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAA;IACnC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,CAAC,KAAK,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3C,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YAC9B,CAAC;YACD,GAAG,CAAC,SAAS,IAAI,KAAK,CAAC,SAAS,CAAA;QAClC,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
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package/esm/pairwise.js
CHANGED
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@@ -1,7 +1,15 @@
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1
1
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import { getFirstNonEmptyLine } from "./util.js";
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function isRulerLine(line) {
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const trimmed = line.trim();
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if (!trimmed) {
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return false;
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}
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const fields = trimmed.split(/\s+/);
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return fields.every(f => /^\d+$/.test(f));
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}
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function isSequenceLine(line) {
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const trimmed = line.trim();
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return /^\w+\s+/.test(trimmed);
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return /^\w+\s+/.test(trimmed) && !isRulerLine(line);
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}
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function hasPositionNumbers(fields) {
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return fields.length >= 3 && /^\d+$/.test(fields[1]);
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@@ -22,7 +30,10 @@ export function parsePairwiseBlock(arr) {
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return undefined;
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}
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while (line) {
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if (
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if (isRulerLine(line)) {
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// skip position ruler lines
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}
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else if (isSequenceLine(line)) {
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block.push(line);
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}
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else {
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package/esm/pairwise.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"pairwise.js","sourceRoot":"","sources":["../src/pairwise.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,WAAW,CAAA;AAEhD,SAAS,cAAc,CAAC,IAAY;IAClC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,OAAO,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;
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1
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{"version":3,"file":"pairwise.js","sourceRoot":"","sources":["../src/pairwise.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,WAAW,CAAA;AAEhD,SAAS,WAAW,CAAC,IAAY;IAC/B,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,OAAO,KAAK,CAAA;IACd,CAAC;IACD,MAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IACnC,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;AAC3C,CAAC;AAED,SAAS,cAAc,CAAC,IAAY;IAClC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,OAAO,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;AACtD,CAAC;AAED,SAAS,kBAAkB,CAAC,MAAgB;IAC1C,OAAO,MAAM,CAAC,MAAM,IAAI,CAAC,IAAI,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;AACtD,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,IAAY,EAAE,QAAgB;IACzD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IACnC,MAAM,GAAG,GAAG,MAAM,CAAC,QAAQ,CAAC,CAAA;IAC5B,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAA;IAC9E,OAAO,CAAC,QAAQ,EAAE,QAAQ,GAAG,GAAG,CAAC,MAAM,CAAU,CAAA;AACnD,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,kBAAkB,CAAC,GAAqB;IACtD,IAAI,IAAI,GAAG,oBAAoB,CAAC,GAAG,CAAC,CAAA;IACpC,MAAM,KAAK,GAAa,EAAE,CAAA;IAC1B,IAAI,aAAa,GAAG,EAAE,CAAA;IACtB,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,OAAO,IAAI,EAAE,CAAC;QACZ,IAAI,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC;YACtB,4BAA4B;QAC9B,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,CAAC;YACN,aAAa,GAAG,IAAI,CAAA;QACtB,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;IACzB,CAAC;IAED,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAA;IACpD,MAAM,QAAQ,GAAG,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACtD,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;IACrD,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAA;IACzC,IAAI,SAAS,GAAG,aAAa,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAE/C,0DAA0D;IAC1D,MAAM,SAAS,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;IACnD,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;QAClB,SAAS,IAAI,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,CAAA;IACpC,CAAC;IACD,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,SAAS,EAAE,CAAA;AACjC,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,GAAqB;IACvD,IAAI,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAA;IACnC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,CAAC,KAAK,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3C,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YAC9B,CAAC;YACD,GAAG,CAAC,SAAS,IAAI,KAAK,CAAC,SAAS,CAAA;QAClC,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
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package/package.json
CHANGED
package/src/pairwise.ts
CHANGED
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@@ -1,8 +1,17 @@
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1
1
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import { getFirstNonEmptyLine } from './util.ts'
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2
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3
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function isRulerLine(line: string) {
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const trimmed = line.trim()
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if (!trimmed) {
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return false
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}
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const fields = trimmed.split(/\s+/)
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return fields.every(f => /^\d+$/.test(f))
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}
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function isSequenceLine(line: string) {
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const trimmed = line.trim()
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-
return /^\w+\s+/.test(trimmed)
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return /^\w+\s+/.test(trimmed) && !isRulerLine(line)
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}
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function hasPositionNumbers(fields: string[]) {
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@@ -27,7 +36,9 @@ export function parsePairwiseBlock(arr: Iterator<string>) {
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}
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while (line) {
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if (
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if (isRulerLine(line)) {
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40
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// skip position ruler lines
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41
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} else if (isSequenceLine(line)) {
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block.push(line)
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32
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} else {
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consensusLine = line
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