@gmod/cram 2.0.2 → 2.0.4

package/src/indexedCramFile.ts

@@ -1,5 +1,4 @@
-import { CramSizeLimitError, CramUnimplementedError } from './errors'
-
+import { CramUnimplementedError } from './errors'
 import CramFile from './cramFile'
 import CramRecord from './cramFile/record'
 import { SeqFetch } from './cramFile/file'
@@ -24,7 +23,6 @@ export interface CramIndexLike {
 export default class IndexedCramFile {
   public cram: CramFile
   public index: CramIndexLike
-  private fetchSizeLimit: number
 
   /**
    *
@@ -32,14 +30,12 @@ export default class IndexedCramFile {
    * @param {CramFile} args.cram
    * @param {Index-like} args.index object that supports getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
    * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
-   * @param {number} [args.fetchSizeLimit] optional maximum number of bytes to fetch in a single getRecordsForRange call.  Default 3 MiB.
    * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
    * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
    */
   constructor(
     args: {
       index: CramIndexLike
-      fetchSizeLimit?: number
     } & (
       | { cram: CramFile }
       | ({
@@ -70,8 +66,6 @@ export default class IndexedCramFile {
     if (!this.index.getEntriesForRange) {
       throw new Error('invalid arguments: not an index')
     }
-
-    this.fetchSizeLimit = args.fetchSizeLimit || 3000000
   }
 
   /**
@@ -103,12 +97,6 @@ export default class IndexedCramFile {
     }
     const seqId = seq
     const slices = await this.index.getEntriesForRange(seqId, start, end)
-    const totalSize = slices.map(s => s.sliceBytes).reduce((a, b) => a + b, 0)
-    if (totalSize > this.fetchSizeLimit) {
-      throw new CramSizeLimitError(
-        `data size of ${totalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`,
-      )
-    }
 
     // TODO: do we need to merge or de-duplicate the blocks?
 
@@ -180,17 +168,7 @@ export default class IndexedCramFile {
 
       const mateRecordPromises = []
       const mateFeatPromises: Promise<CramRecord[]>[] = []
-
-      const mateTotalSize = mateChunks
-        .map(s => s.sliceBytes)
-        .reduce((a, b) => a + b, 0)
-      if (mateTotalSize > this.fetchSizeLimit) {
-        throw new Error(
-          `mate data size of ${mateTotalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`,
-        )
-      }
-
-      mateChunks.forEach(c => {
+      for (const c of mateChunks) {
         let recordPromise = this.cram.featureCache.get(c.toString())
         if (!recordPromise) {
           recordPromise = this.getRecordsInSlice(c, () => true)
@@ -210,7 +188,7 @@ export default class IndexedCramFile {
           return mateRecs
         })
         mateFeatPromises.push(featPromise)
-      })
+      }
       const newMateFeats = await Promise.all(mateFeatPromises)
       if (newMateFeats.length) {
         const newMates = newMateFeats.reduce((result, current) =>

package/src/io/index.ts

@@ -1,16 +1,6 @@
-import url from 'url'
-import { ensureNotNullish } from '../typescript'
 import { Filehandle } from '../cramFile/filehandle'
 import { LocalFile, RemoteFile } from 'generic-filehandle'
 
-function fromUrl(source: string) {
-  const { protocol, pathname } = url.parse(source)
-  if (protocol === 'file:') {
-    return new LocalFile(unescape(ensureNotNullish(pathname)))
-  }
-  return new RemoteFile(source)
-}
-
 function open(
   maybeUrl?: string,
   maybePath?: string,
@@ -20,7 +10,7 @@ function open(
     return maybeFilehandle
   }
   if (maybeUrl) {
-    return fromUrl(maybeUrl)
+    return new RemoteFile(maybeUrl)
   }
   if (maybePath) {
     return new LocalFile(maybePath)
@@ -28,6 +18,6 @@ function open(
   throw new Error('no url, path, or filehandle provided, cannot open')
 }
 
-export { fromUrl, open }
+export { open }
 
 export { LocalFile, RemoteFile } from 'generic-filehandle'

package/src/sam.ts

@@ -4,7 +4,7 @@ export function parseHeaderText(text: string) {
     tag: string
     data: {
       tag: string
-      value: string | undefined
+      value: string
     }[]
   }[] = []
   for (const line of lines) {
@@ -21,10 +21,10 @@ export function parseHeaderText(text: string) {
               }
             : // @CO lines are not comma separated.
               // See "samtools view -H c2\#pad.3.0.cram"
-              // so, just store value tag itself
+              // so, just store value tag and value itself
               {
                 tag: f,
-                value: undefined,
+                value: '',
               }
         }),
       })

package/src/typescript.ts

@@ -1,10 +1,3 @@
-export function ensureNotNullish<T>(x: T | null | undefined): T {
-  if (x === null || x === undefined) {
-    throw new Error('Value must not be nullish.')
-  }
-  return x
-}
-
 export type TupleOf<T, N extends number> = N extends N
   ? number extends N
     ? T[]