A CGI-version of samtools tview.

I've created a lightweight CGI-based web-application for samtools tview. This C++ program named ngsproject.cgi uses the samtools api, it allows any user to visualize all the alignments in a given NGS project. The projects and their BAMS are defined on the server side using a simple XML document. e.g:

<?xml version="1.0"?>
<projects>
 <reference id="hg19">
  <path>/home/lindenb/samtools-0.1.18/examples/ex1.fa</path>
 </reference>
 <bam id="b1">
  <sample>Sample 1</sample>
  <path>/home/lindenb/samtools-0.1.18/examples/ex1.bam</path>
 </bam>
 <bam id="b2">
  <sample>Sample 2</sample>
  <path>/home/lindenb/samtools-0.1.18/examples/ex1.bam</path>
 </bam>
 <project id="1">
  <name>Test 1</name>
  <description>Test</description>
  <bam ref="b1"/>
  <bam ref="b2"/>
  <reference ref="hg19" />
 </project>
 <project id="2">
  <name>Test 2</name>
  <description>Test</description>
  <bam ref="b2"/>
  <reference ref="hg19" />
 </project>
</projects>

Once the CGI has been installed, the user can visualize the reads of each samples.

This tool is available in the variation toolkit at http://code.google.com/p/variationtoolkit/.

That's it.

Pierre