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, 14:54, 29 August 2011
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| === Using github === | | === Using github === |
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− | 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]]. |
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| ==== Using Git To Track the Current Development Version ==== | | ==== Using Git To Track the Current Development Version ==== |
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| == 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. |
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− | On github, you can both browse and download the latest version of the library, as well as explore the history of changes.
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− | You can access the latest version with or without using git.
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− | [edit]
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| + | == Programs == |
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| 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. |
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| * [[C++ Executable: bam#diff|diff - Print the diffs between 2 bams]] | | * [[C++ Executable: bam#diff|diff - Print the diffs between 2 bams]] |
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− | This executable is built using [[StatGenLibrary: BAM]]. | + | This executable is built using [[C++ Library: libStatGen]]. |
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| Just running ./bam will print the Usage information for the bam executable. | | Just running ./bam will print the Usage information for the bam executable. |
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| 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. |
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− | 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: |
− | ./bam --in <bamFile>.bam --out <newSamFile>.sam | + | <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. |
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