diff --git a/README.md b/README.md index 90f9856..a78c2dd 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ const { IndexedFasta, BgzipIndexedFasta } = require('@gmod/indexedfasta') // this uses local file paths for node.js for IndexedFasta, for usages using // remote URLs see indexedfasta docs for filehandles and -// https://github.com/gmod/generic-filehandle +// https://github.com/gmod/generic-filehandle2 const t = new IndexedFasta({ path: '/filesystem/yourfile.fa', faiPath: '/filesystem/yourfile.fa.fai', @@ -56,18 +56,18 @@ run = async () => { // // alternatively `cramFilehandle` (for the IndexedCramFile class) and // `filehandle` (for the CraiIndex) can be used, see for examples - // https://github.com/gmod/generic-filehandle + // https://github.com/gmod/generic-filehandle2 const indexedFile = new IndexedCramFile({ cramPath: '/filesystem/yourfile.cram', //or //cramUrl: 'url/to/file.cram' - //cramFilehandle: a generic-filehandle or similar filehandle + //cramFilehandle: a generic-filehandle2 or similar filehandle index: new CraiIndex({ path: '/filesystem/yourfile.cram.crai', // or // url: 'url/to/file.cram.crai' - // filehandle: a generic-filehandle or similar filehandle + // filehandle: a generic-filehandle2 or similar filehandle }), seqFetch: async (seqId, start, end) => { // note: @@ -82,7 +82,7 @@ run = async () => { const samHeader = await indexedFile.cram.getSamHeader() // use the @SQ lines in the header to figure out the - // mapping between ref ref ID numbers and names + // mapping between ref ID numbers and names const sqLines = samHeader.filter(l => l.tag === 'SQ') sqLines.forEach((sqLine, refId) => { @@ -120,7 +120,7 @@ run = async () => { run() // can also pass `cramUrl` (for the IndexedCramFile class), and `url` (for the CraiIndex) params to open remote URLs -// alternatively `cramFilehandle` (for the IndexedCramFile class) and `filehandle` (for the CraiIndex) can be used, see for examples https://github.com/gmod/generic-filehandle +// alternatively `cramFilehandle` (for the IndexedCramFile class) and `filehandle` (for the CraiIndex) can be used, see for examples https://github.com/gmod/generic-filehandle2 ``` You can use cram-js without NPM also with the cram-bundle.js. See the example