Week 0: Planning

The main goal of the BAM File Viewer for BioJS is to display the NGS alignments of regions in a reference. To be effective, it will be integrated with the BioJS FeatureViewer. The base implementation will be based on the BAM viewer widget in the TGAC Browser, but it is going to be extended to support the missing BAM flags in the current implementation. BAM files are too big to be kept in memory at once. Traditional visualisation programs only keep in memory the region to be displayed. To mimic this behavior, a reference implementation of a web server that extract manageable regions will be implemented in Java on the top of the Java-Genomics-IO API. However, the SAM parsing will be implemented in the client, enabling other server technologies to be used to query the regions in the BAM File.

The tasks to implement are:

• SAM Parser. From the TAB file to JSON 
• A minimal web server which queries regions, using the conventions of samtools 
• Extract the TGAC browser BAM widget from the browser 
• Design and implement the missing SAM flags 
• Ιmplement BioJS events API 
• Integrate with FeatureViewer/BigWig 

So, the overall design of the component is better understood in the following diagram. 

During the GSoC 2014 I will focus on implementing a single reference server in the initial stage.