Misc

GMOD · Aug 21, 2024 · acb1661 · acb1661
1 parent 5dfa77f
commit acb1661
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Showing 4 changed files with 22 additions and 24 deletions.
diff --git a/test/cram2sam.ts b/test/cram2sam.ts
@@ -1,8 +1,9 @@
+/* eslint-disable no-console */
 import { IndexedFasta } from '@gmod/indexedfasta'
 import { CraiIndex, IndexedCramFile } from '../src'
 import CramRecord from '../src/cramFile/record'
 
-if (process.argv.length != 7) {
+if (process.argv.length !== 7) {
   process.stderr.write(
     'Usage: node jkb_test.js REF.fa input.cram tid start end\n',
   )
@@ -19,14 +20,14 @@ const end = Number.parseInt(endStr)
 // Fasta
 const t = new IndexedFasta({
   path: process.argv[2],
-  faiPath: process.argv[2] + '.fai',
+  faiPath: `${process.argv[2]}.fai`,
 })
 
 // open local files
 const indexedFile = new IndexedCramFile({
   cramPath: process.argv[3],
   index: new CraiIndex({
-    path: process.argv[3] + '.crai',
+    path: `${process.argv[3]}.crai`,
   }),
   seqFetch: async (seqId, start, end) => {
     // note:
@@ -60,7 +61,7 @@ function decodeSeqCigar(record: CramRecord) {
       seq += ref.slice(last_pos - refStart, refPos - refStart)
       last_pos = refPos
 
-      if (oplen && op != 'M') {
+      if (oplen && op !== 'M') {
         cigar += oplen + op
         oplen = 0
       }
@@ -86,53 +87,53 @@ function decodeSeqCigar(record: CramRecord) {
         seq += sub
         last_pos++
         oplen++
-      } else if (code == 'D' || code == 'N') {
+      } else if (code === 'D' || code === 'N') {
         // Deletion or Ref Skip
         last_pos += data
         if (oplen) {
           cigar += oplen + op
         }
         cigar += data + code
         oplen = 0
-      } else if (code == 'I' || code == 'S') {
+      } else if (code === 'I' || code === 'S') {
         // Insertion or soft-clip
         seq += data
         if (oplen) {
           cigar += oplen + op
         }
         cigar += data.length + code
         oplen = 0
-      } else if (code == 'i') {
+      } else if (code === 'i') {
         // Single base insertion
         seq += data
         if (oplen) {
           cigar += oplen + op
         }
-        cigar += 1 + 'I'
+        cigar += `${1}I`
         oplen = 0
-      } else if (code == 'P') {
+      } else if (code === 'P') {
         // Padding
         if (oplen) {
           cigar += oplen + op
         }
-        cigar += data + 'P'
-      } else if (code == 'H') {
+        cigar += `${data}P`
+      } else if (code === 'H') {
         // Hard clip
         if (oplen) {
           cigar += oplen + op
         }
-        cigar += data + 'H'
+        cigar += `${data}H`
         oplen = 0
       } // else q or Q
     })
   } else {
     sublen = record.readLength - seq.length
   }
-  if (seq.length != record.readLength) {
+  if (seq.length !== record.readLength) {
     sublen = record.readLength - seq.length
     seq += ref.slice(last_pos - refStart, last_pos - refStart + sublen)
 
-    if (oplen && op != 'M') {
+    if (oplen && op !== 'M') {
       cigar += oplen + op
       oplen = 0
     }
@@ -168,7 +169,7 @@ function tags2str(record: CramRecord, RG: string[]) {
   }
 
   if (record.readGroupId >= 0) {
-    str += '\tRG:Z:' + RG[record.readGroupId]
+    str += `\tRG:Z:${RG[record.readGroupId]}`
   }
   return str
 }
@@ -179,16 +180,13 @@ async function run() {
   const seqList = await t.getSequenceNames()
   let tid: string | number = chr // ie numeric or string form
   seqList.forEach((name, id) => {
-    if (name == chr) {
+    if (name === chr) {
       tid = id
       return
     }
   })
 
   const hdr = await indexedFile.cram.getSamHeader()
-  if (!hdr) {
-    throw new Error('getSamHeader returned undefined')
-  }
   const RG: string[] = []
   let nRG = 0
   for (const line of hdr) {

diff --git a/test/example-code.test.ts b/test/example-code.test.ts
@@ -12,9 +12,9 @@ describe('code examples', () => {
 
       // or with local files
       const indexedFile2 = new IndexedCramFile({
-        cramPath: require.resolve(`./data/ce#5.tmp.cram`),
+        cramPath: require.resolve("./data/ce#5.tmp.cram"),
         index: new CraiIndex({
-          path: require.resolve(`./data/ce#5.tmp.cram.crai`),
+          path: require.resolve("./data/ce#5.tmp.cram.crai"),
         }),
         seqFetch: async (seqId, start, end) => {
           let fakeSeq = ''

diff --git a/test/lib/syncLocalFile.ts b/test/lib/syncLocalFile.ts
@@ -12,7 +12,7 @@ class LocalFile {
     this.filename = source
   }
 
-  async read(buffer, offset = 0, length, position) {
+  async read(buffer, offset, length, position) {
     let readPosition = position
     if (readPosition === null) {
       readPosition = this.position

diff --git a/test/lossy-names.test.ts b/test/lossy-names.test.ts
@@ -4,9 +4,9 @@ import { CraiIndex, IndexedCramFile } from '../src'
 describe('1kg mate test', () => {
   it('runs without error', async () => {
     const indexedCramFile = new IndexedCramFile({
-      cramPath: require.resolve(`./data/na12889_lossy.cram`),
+      cramPath: require.resolve("./data/na12889_lossy.cram"),
       index: new CraiIndex({
-        path: require.resolve(`./data/na12889_lossy.cram.crai`),
+        path: require.resolve("./data/na12889_lossy.cram.crai"),
       }),
       seqFetch: async (seqId, start, end) => {
         let fakeSeq = ''