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bam utility js library that supports both local (via harddrive) and remote (via url) bam files. We use a combination of javascript methods and iobio webservices

JavaScript 100.00%

bam.iobio.js's Introduction

Usage

// create bam object with either an http url to a bam or a html5 FILE object
var bam = new Bam( bamUrl );
var bam = new Bam( bamFile , { bai: baiFile });

// Fetch region
// bam.fetch( name, start, end, callback );
// where name is chromosome or sequence name
// start and end are region coordinates, 
// callback is what handles the returned data
bam.fetch("chr1", 2000000, 250000, function(records) {
// do something with records
})
 
// fetch as sam format
bam.convert("sam", "chr1", 2000000, 250000, function(records) {
// do something with records
})

bam.iobio.js's People

Contributors

chmille4 avatar

Stargazers

 avatar Jayson Harshbarger avatar

Watchers

 avatar  avatar James Cloos avatar

bam.iobio.js's Issues

serve local bam file in binary

Currently when a local bam file needs to be sent out to a webservice the necessary regions are extracted into sam format and then sent to a webservice to convert it into bam format before being sent on to have work done on it. It would be more efficient to determine how to send the appropriate number of bytes that is the header and the desired reads.

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