Security News
Research
Data Theft Repackaged: A Case Study in Malicious Wrapper Packages on npm
The Socket Research Team breaks down a malicious wrapper package that uses obfuscation to harvest credentials and exfiltrate sensitive data.
$ npm install --save @gmod/bam
const {BamFile} = require('@gmod/bam');
const t = new BamFile({
bamPath: 'test.bam',
});
var header = await t.getHeader()
var records = await t.getRecordsForRange('ctgA', 1, 50000)
Input are 0-based half-open coordinates (note: not the same as samtools view coordinate inputs!)
The BAM class constructor accepts arguments
Note: filehandles implement the Filehandle interface from https://www.npmjs.com/package/generic-filehandle. This module offers the path and url arguments as convenience methods for supplying the LocalFile and RemoteFile
Returns features of the form {start, end, score} containing estimated feature density across 16kb windows in the genome
The returned features from BAM are lazy features meaning that it delays processing of all the feature tags until necessary.
You can access data feature.get('field') to get the value of a feature attribute
Example
feature.get('seq_id') // numerical sequence id corresponding to position in the sam header
feature.get('start') // 0 based half open start coordinate
feature.get('end') // 0 based half open end coordinate
feature.get('name') // QNAME
feature.get('seq') // feature sequence
feature.get('qual') // qualities
feature.get('cigar') // cigar string
feature.get('MD') // MD string
feature.get('SA') // supplementary alignments
feature.get('template_length') // TLEN
feature.get('length_on_ref') // derived from CIGAR using standard algorithm
feature.get('seq_reverse_complemented')
feature.get('unmapped')
feature.get('qc_failed')
feature.get('duplicate')
feature.get('secondary_alignment')
feature.get('supplementary_alignment')
The feature format may change in future versions to be more raw records but will be a major version bump
MIT © Colin Diesh
1.0.17 (2019-04-28)
FAQs
Parser for BAM and BAM index (bai) files
The npm package @gmod/bam receives a total of 1,839 weekly downloads. As such, @gmod/bam popularity was classified as popular.
We found that @gmod/bam demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 0 open source maintainers collaborating on the project.
Did you know?
Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.
Security News
Research
The Socket Research Team breaks down a malicious wrapper package that uses obfuscation to harvest credentials and exfiltrate sensitive data.
Research
Security News
Attackers used a malicious npm package typosquatting a popular ESLint plugin to steal sensitive data, execute commands, and exploit developer systems.
Security News
The Ultralytics' PyPI Package was compromised four times in one weekend through GitHub Actions cache poisoning and failure to rotate previously compromised API tokens.