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=== Using github ===
=== 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:_libStatGen|Get libStatGen]].
If you download from github or use git to keep up to date, you also need <code>libStatGen</code>. [[C++ Library: libStatGen|Get libStatGen]].
==== Using Git To Track the Current Development Version ====
==== Using Git To Track the Current Development Version ====
== Building ==
== 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 bamUtil/bin/ directory.
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.
== 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.
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]]
* [[C++ Executable: bam#diff|diff - Print the diffs between 2 bams]]
This executable is built using [[StatGenLibrary: BAM]].
This executable is built using [[C++ Library: libStatGen]].
Just running ./bam will print the Usage information for the bam executable.
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 <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:
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, 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.
Don't forget to put in the paths to the executable and your test files.
