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361 bytes removed
, 01:34, 2 November 2010
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| [[Category:Software]] | | [[Category:Software]] |
| [[Category:C++]] | | [[Category:C++]] |
− | [[Category:libbam]] | + | [[Category:BAM Classes]] |
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| = SAM/BAM File= | | = SAM/BAM File= |
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− | See [[C++ Library: libbam Change Log]] for a list of the most recent updates to the library. | + | See [[C++ Library: BAM Change Log]] for a list of the most recent updates to the BAM classes. |
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| [[BAM Review Action Items]] | | [[BAM Review Action Items]] |
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− | == Read & Write BAM/SAM Library == | + | == Read & Write BAM/SAM Library Software == |
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| The software reads the beginning of files opened for reading to determine if it is SAM/BAM. To determine the format (SAM/BAM) of files open for writing, 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 files opened for reading to determine if it is SAM/BAM. To determine the format (SAM/BAM) of files open for writing, 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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− | The library is found in pipeline/bam, and is called libbam.a. | + | The library is found in statgen/lib/bam. |
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− | This library is dependent on two other libraries:
| + | === BAM/SAM Classes === |
− | # [[C++ Library: libcsg|libcsg/libcsg.a]]
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− | # thirdParty/samtools/libbam.a
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− | '''Be sure to include them all in the proper order:'''
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− | <path to base pipeline directory>/libbam.a <path to base pipeline directory>/libcsg/libcsg.a <path to base pipeline directory>/thirdParty/samtools/libbam.a
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− | === Classes in the BAM/SAM Library === | |
| {| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | | {| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" |
| |-style="background: #f2f2f2; text-align: center;" | | |-style="background: #f2f2f2; text-align: center;" |
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| == FAQs == | | == FAQs == |
− | [[SAM/BAM Library FAQs]] | + | [[SAM/BAM Classes FAQs]] |
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| == Usage Examples == | | == Usage Examples == |
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| == Suggested Improvements/Features == | | == Suggested Improvements/Features == |
− | See [[C++ Library: libbam Change Log#Known Issues|Change Log]] | + | See [[C++ Library: BAM Change Log#Known Issues|Change Log]] |