updating husky

TeselaGen · Feb 27, 2023 · 4114a81 · 4114a81
1 parent def4e99
commit 4114a81
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Showing 4 changed files with 31 additions and 35 deletions.
diff --git a/.husky/pre-commit b/.husky/pre-commit
@@ -0,0 +1,4 @@
+#!/usr/bin/env sh
+. "$(dirname -- "$0")/_/husky.sh"
+
+yarn lint-staged && yarn test
diff --git a/package.json b/package.json
@@ -51,7 +51,7 @@
     "chai-subset": "^1.1.0",
     "eslint": "8.35.0",
     "eslint-config-teselagen": "6.0.16",
-    "husky": "^0.11.6",
+    "husky": "^8.0.3",
     "jest": "^29.4.3",
     "jsonfile": "^2.3.1",
     "lint-staged": "^9.2.1",

diff --git a/src/addGapsToSeqReads.js b/src/addGapsToSeqReads.js
@@ -21,12 +21,12 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
 
   const refSeqWithGaps = insertGapsIntoRefSeq(refSeq.sequence, seqReads);
   // first object is reference sequence with gaps, to be followed by seq reads with gaps
-  let seqReadsWithGaps = [
+  const seqReadsWithGaps = [
     { name: refSeq.name, sequence: refSeqWithGaps.toUpperCase() }
   ];
   seqReads.forEach(seqRead => {
     // get all insertions in seq reads
-    let allInsertionsInSeqReads = [];
+    const allInsertionsInSeqReads = [];
     seqReads.forEach(seqRead => {
       // split cigar string at S, M, D, or I (soft-clipped, match, deletion, or insertion), e.g. ["5S", "2M", "3I", "39M", "3D"..."9S"]
       const splitSeqRead = seqRead.cigar.match(/([0-9]*[SMDI])/g);
@@ -51,7 +51,7 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
               bpPosOfInsertion += previousComponentNumber;
             }
           }
-          let insertionInfo = {
+          const insertionInfo = {
             // keeping bpPos 1-based
             bpPos: bpPosOfInsertion,
             number: numberOfInsertions
@@ -77,7 +77,7 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
 
     // 2) add own deletions to own sequence
     // get own deletions
-    let ownDeletions = [];
+    const ownDeletions = [];
     for (
       let componentI = 0;
       componentI < splitSeqReadChunk.length;
@@ -94,7 +94,7 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
           );
           bpPosOfDeletion += previousComponentNumber;
         }
-        let deletionInfo = {
+        const deletionInfo = {
           // keeping bpPos 1-based
           bpPos: bpPosOfDeletion,
           number: numberOfDeletions
@@ -103,7 +103,7 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
       }
     }
     // sort deletions by ascending bp pos
-    let sortedOwnDeletions = ownDeletions.sort(function(a, b) {
+    const sortedOwnDeletions = ownDeletions.sort(function(a, b) {
       return a.bpPos - b.bpPos;
     });
     // add own deletions to own sequence
@@ -122,8 +122,8 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
 
     // 3) remove own insertions from own sequence
     // get own insertions
-    let ownInsertions = [];
-    let ownInsertionsBp = [];
+    const ownInsertions = [];
+    const ownInsertionsBp = [];
     for (
       let componentI = 0;
       componentI < splitSeqReadChunk.length;
@@ -134,7 +134,7 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
         const numberOfInsertions = Number(
           splitSeqReadChunk[componentI].slice(0, -1)
         );
-        let nucleotides = [];
+        const nucleotides = [];
         for (let i = 0; i < componentI; i++) {
           const previousComponentNumber = Number(
             splitSeqReadChunk[i].slice(0, -1)
@@ -144,12 +144,12 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
         for (let nucI = 0; nucI < numberOfInsertions; nucI++) {
           nucleotides.push(eachSeqReadWithGaps[bpPosOfInsertion - 1 + nucI]);
         }
-        let insertionInfo = {
+        const insertionInfo = {
           // keeping bpPos 1-based
           bpPos: bpPosOfInsertion,
           number: numberOfInsertions
         };
-        let insertionInfoBp = {
+        const insertionInfoBp = {
           // keeping bpPos 1-based
           bpPos: bpPosOfInsertion,
           number: numberOfInsertions,
@@ -159,12 +159,12 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
         ownInsertionsBp.push(insertionInfoBp);
       }
     }
-    let ownInsertionsCompare = JSON.parse(JSON.stringify(ownInsertions));
+    const ownInsertionsCompare = JSON.parse(JSON.stringify(ownInsertions));
     // sort own insertions by ascending bp pos
-    let sortedOwnInsertions = ownInsertions.sort(function(a, b) {
+    const sortedOwnInsertions = ownInsertions.sort(function(a, b) {
       return a.bpPos - b.bpPos;
     });
-    let sortedOwnInsertionsBp = ownInsertionsBp.sort(function(a, b) {
+    const sortedOwnInsertionsBp = ownInsertionsBp.sort(function(a, b) {
       return a.bpPos - b.bpPos;
     });
     // remove own insertions from own sequence
@@ -210,7 +210,7 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
     }
     // then remove own insertions from all insertions
     for (let otherI = 0; otherI < ownInsertionsCompare.length; otherI++) {
-      let insertionInfoIndex = otherInsertions.findIndex(
+      const insertionInfoIndex = otherInsertions.findIndex(
         e => e.bpPos === ownInsertionsCompare[otherI].bpPos
       );
       if (insertionInfoIndex !== -1) {
@@ -232,7 +232,7 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
     }
     // then combine overlap between other insertions & own insertions
     for (let overlapI = 0; overlapI < sortedOwnInsertions.length; overlapI++) {
-      let insertionInfoIndex = otherInsertions.findIndex(
+      const insertionInfoIndex = otherInsertions.findIndex(
         e => e.bpPos === sortedOwnInsertions[overlapI].bpPos
       );
       if (insertionInfoIndex !== -1) {
@@ -253,7 +253,7 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
       }
     }
     // adjust own insertions according to other seq reads' insertions to be added (i.e. for all other reads' insertions with smaller bp pos, +1 to that own insertion's bp pos)
-    let adjustedOwnInsertionsBp = JSON.parse(
+    const adjustedOwnInsertionsBp = JSON.parse(
       JSON.stringify(sortedOwnInsertionsBp)
     );
     for (let ownI = 0; ownI < adjustedOwnInsertionsBp.length; ownI++) {
@@ -322,7 +322,7 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
   // 7) add gaps before starting bp pos
   // add gaps based on any seq reads that extend beyond beginning of the ref seq due to soft-clipped reads
   // a) get the lengths of bps that extend beyond the beginning of the ref seq among all seq reads
-  let seqReadLengthsBeforeRefSeqStart = [];
+  const seqReadLengthsBeforeRefSeqStart = [];
   seqReads.forEach(seq => {
     const splitSeqReadChunk = seq.cigar.match(/([0-9]*[SMDI])/g);
     let adjustedSeqReadPos = cloneDeep(seq.pos);
@@ -344,7 +344,7 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
   let longestSeqReadLength = 0;
   for (let i = 1; i < seqReadsWithGaps.length; i++) {
     // turn seq read into an array ["A", "T", "C", "G"...]
-    let eachSeqReadWithGaps = seqReadsWithGaps[i].sequence.split("");
+    const eachSeqReadWithGaps = seqReadsWithGaps[i].sequence.split("");
     const splitSeqReadChunk = seqReads[i - 1].cigar.match(/([0-9]*[SMDI])/g);
     let adjustedSeqReadPos = cloneDeep(seqReads[i - 1].pos);
     // longest length of bps that extend beyond the beginning of the ref seq among all seq reads
@@ -378,13 +378,13 @@ module.exports = function addGapsToSeqReads(refSeq, seqReads) {
 
   // add gaps before ref seq based on the longest length of soft-clipped reads that extend beyond beginning of ref seq
   if (longestSeqReadLength > 0) {
-    let splitRefSeqWithGaps = seqReadsWithGaps[0].sequence.split("");
+    const splitRefSeqWithGaps = seqReadsWithGaps[0].sequence.split("");
     splitRefSeqWithGaps.unshift("-".repeat(longestSeqReadLength + 1));
     seqReadsWithGaps[0].sequence = splitRefSeqWithGaps.join("");
   }
 
   // 8) check if any seq read is longer than the ref seq, make ref seq & seq reads all the same length
-  let lengthsOfLongerSeqReads = [];
+  const lengthsOfLongerSeqReads = [];
   for (let i = 1; i < seqReadsWithGaps.length; i++) {
     const refSeq = seqReadsWithGaps[0];
     if (seqReadsWithGaps[i].sequence.length > refSeq.sequence.length) {

diff --git a/yarn.lock b/yarn.lock
@@ -6945,13 +6945,10 @@ human-signals@^2.1.0:
   resolved "https://registry.yarnpkg.com/human-signals/-/human-signals-2.1.0.tgz#dc91fcba42e4d06e4abaed33b3e7a3c02f514ea0"
   integrity sha512-B4FFZ6q/T2jhhksgkbEW3HBvWIfDW85snkQgawt07S7J5QXTk6BkNV+0yAeZrM5QpMAdYlocGoljn0sJ/WQkFw==
 
-husky@^0.11.6:
-  version "0.11.9"
-  resolved "https://registry.yarnpkg.com/husky/-/husky-0.11.9.tgz#28cd1dc16bffdca1d4d93592814e5f3c327b38ee"
-  integrity sha1-KM0dwWv/3KHU2TWSgU5fPDJ7OO4=
-  dependencies:
-    is-ci "^1.0.9"
-    normalize-path "^1.0.0"
+husky@^8.0.3:
+  version "8.0.3"
+  resolved "https://registry.yarnpkg.com/husky/-/husky-8.0.3.tgz#4936d7212e46d1dea28fef29bb3a108872cd9184"
+  integrity sha512-+dQSyqPh4x1hlO1swXBiNb2HzTDN1I2IGLQx1GrBuiqFJfoMrnZWwVmatvSiO+Iz8fBUnf+lekwNo4c2LlXItg==
 
 [email protected]:
   version "0.4.15"
@@ -7291,7 +7288,7 @@ is-callable@^1.2.7:
   resolved "https://registry.yarnpkg.com/is-callable/-/is-callable-1.2.7.tgz#3bc2a85ea742d9e36205dcacdd72ca1fdc51b055"
   integrity sha512-1BC0BVFhS/p0qtw6enp8e+8OD0UrK0oFLztSjNzhcKA3WDuJxxAPXzPuPtKkjEY9UUoEWlX/8fgKeu2S8i9JTA==
 
-is-ci@^1.0.10, is-ci@^1.0.8, is-ci@^1.0.9:
+is-ci@^1.0.10, is-ci@^1.0.8:
   version "1.2.1"
   resolved "https://registry.yarnpkg.com/is-ci/-/is-ci-1.2.1.tgz#e3779c8ee17fccf428488f6e281187f2e632841c"
   integrity sha512-s6tfsaQaQi3JNciBH6shVqEDvhGut0SUXr31ag8Pd8BBbVVlcGfWhpPmEOoM6RJ5TFhbypvf5yyRw/VXW1IiWg==
@@ -9593,11 +9590,6 @@ normalize-package-data@^2.3.2, normalize-package-data@^2.3.4:
     semver "2 || 3 || 4 || 5"
     validate-npm-package-license "^3.0.1"
 
-normalize-path@^1.0.0:
-  version "1.0.0"
-  resolved "https://registry.yarnpkg.com/normalize-path/-/normalize-path-1.0.0.tgz#32d0e472f91ff345701c15a8311018d3b0a90379"
-  integrity sha1-MtDkcvkf80VwHBWoMRAY07CpA3k=
-
 normalize-path@^2.0.0, normalize-path@^2.0.1, normalize-path@^2.1.1:
   version "2.1.1"
   resolved "https://registry.yarnpkg.com/normalize-path/-/normalize-path-2.1.1.tgz#1ab28b556e198363a8c1a6f7e6fa20137fe6aed9"