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BamUtil

69 bytes removed, 14:54, 29 August 2011
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=== Using github ===
If you download from github or use git to keep up to date, you also need <code>libStatGen</code>. [[http://genome.sph.umich.edu/wiki/C%2B%2B_Library++ Library:_libStatGenlibStatGen|Get libStatGen]].
==== Using Git To Track the Current Development Version ====
== Building ==
After obtaining the bamUtil repository (either by download or from github), compile the code using <code>make all</code>. This creates the executable, <code>bam</code>, in the <code>bamUtil/bin/ </code> directory, the debug executable in the <code>bamUtil/bin/debug/</code> directory, and the profiling executable in the <code>bamUtil/bin/profile/</code> directory.
On github, you can both browse and download the latest version of the library, as well as explore the history of changes.
You can access the latest version with or without using git.
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== Programs ==
The software reads the beginning of an input file to determine if it is SAM/BAM. To determine the format (SAM/BAM) of the output file, the software checks the output file's extension. If the extension is ".bam" it writes a BAM file, otherwise it writes a SAM file.
* [[C++ Executable: bam#diff|diff - Print the diffs between 2 bams]]
This executable is built using [[StatGenLibraryC++ Library: BAMlibStatGen]].
Just running ./bam will print the Usage information for the bam executable.
The <code>convert</code> option on the bam executable reads a SAM/BAM file and writes it as a SAM/BAM file.
The executable converts the input file into the format of the output file. So if you want to convert a BAM file to a SAM file, from the pipeline/bam/ directory you just call: .<pathToExe>/bam --in <bamFile>.bam --out <newSamFile>.sam
Don't forget to put in the paths to the executable and your test files.

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