index.html

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layout: layout
title: "BioD home page"
---

<section class="content">
    <h1>Why use BioD for processing BAM data?</h1>

    <section class="why">
    <section class="cword">Terse</section>
    <section class="explanation">
    <p> Most operations require just a few keystrokes, much like in Python, Perl, or Ruby.</p>
        {% highlight d %}
import bio.bam.reader, bio.bam.pileup;
import std.stdio;

void main(string[] args) {
    auto bam = new BamReader(args[1]);
    auto reads = bam["chr2"][500 .. 510];
    foreach (column; reads.makePileup())
        writeln(column.coverage);
}{% endhighlight %}
        </section>
    </section>

    <section class="why">
        <section class="cword">Fast</section>
        <section class="explanation">
        <p>D is a compiled language. As such, it offers speeds close to C++,
        especially when <a href="http://wiki.dlang.org/LDC">LDC</a> or 
        <a href="http://wiki.dlang.org/GDC">GDC</a> compiler is used.</p>
        <p>Many hours were dedicated to code profiling in&nbsp;order&nbsp;to
        make the library as fast as possible, avoiding heap allocations and virtual calls.</p>
        <p>Blocks, from which BAM files consist, are seamlessly packed/unpacked in parallel, employing all CPU cores.</p>
        </section>
    </section>

    <section class="why">
        <section class="cword">Reliable</section>
        <section class="explanation">
        <p>Every non-trivial algorithm in the library is covered by unittests,
        which can be easily run from the command line (see below).</p>
        <p>Whenever you find out that something doesn't work correctly, please
            <a href="http://github.com/biod/biod/issues">report</a> an issue,
            and the test suite will grow once it's fixed!</p>
        </section>
    </section>

    <br />

    <section id="quick-start">
        <section class="cword">Quick start</section>
        <section>
        <table style="padding-left: 20px; margin: 0px 10px 0px 10px;">
            <tbody>
                <tr height="30px">
                    <td width="300px">1. Install DMD compiler</td>
                    <td style="text-align: center">(<a href="http://wiki.dlang.org/Installing_DMD">instructions</a>)</td>
                </tr>
                <tr height="30px">
                    <td>2. Download BioD source code</td>
                    <td> {% highlight sh %}
git clone git://github.com/biod/BioD.git{% endhighlight %}
                    </td>
                </tr>
                <tr height="30px">
                    <td>3. Run unittests</td>
                    <td> {% highlight sh %}
cd BioD/test && rdmd -I.. -unittest unittests.d{% endhighlight %}
                    </td>
                </tr>
                <tr height="30px">
                    <td>4. Run some examples</td>
                    <td> {% highlight sh %}
cd ../examples && rdmd -I.. example1.d{% endhighlight %}
                    </td>
                </tr>
            </tbody>
        </table>
        </section>
        </section>

        <section id="info">
            <section class="info-block">
            <section class="cword kword">License: <font color="black">MIT</font></section>
            </section>
            <section class="info-block">
                <section class="cword kword">Supported platforms:</section>
                <section class="cword">Linux, Mac OS X</section>
            </section>
            <section class="info-block">
                <section class="cword kword">File formats:</section>
                <section class="cword">BAM, SAM, SFF</section>
            </section>
        </section>
</section>