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, 17:35, 7 October 2011
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| = Overview of the <code>squeeze</code> function of <code>bamUtil</code> = | | = Overview of the <code>squeeze</code> function of <code>bamUtil</code> = |
| The <code>squeeze</code> option on the [[bamUtil]] executable reduces files size by optionally: | | The <code>squeeze</code> option on the [[bamUtil]] executable reduces files size by optionally: |
− | * dropping OQ fields | + | * dropping OQ fields (default, disable using <code>--keepOQ</code>) |
− | * dropping duplicates | + | * dropping duplicates (default, disable using <code>--keepDups</code>) |
− | * dropping specified tags | + | * dropping specified tags (<code>--rmTags Tag1:Type1;Tag2:Type2</code>) |
− | * using '=' when a base matches the reference | + | * using '=' when a base matches the reference (<code>--refFile refFileName.fa</code>) |
− | * binning quality scores | + | * binning quality scores (<code>--binQualS</code><code>--binQualF</code>) |
− | * replacing readNames with unique integers | + | * replacing readNames with unique integers (<code>--readName</code>/<code>--sReadName</code>) |
| + | |
| + | |
| + | = Usage = |
| + | ./bam squeeze --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <refFilePath/Name>] [--keepOQ] [--keepDups] [--readName <readNameMapFile.txt>] [--sReadName <readNameMapFile.txt>] [--binQualS <minQualBin2>,<minQualBin3><...>] [--binQualF <filename>] [--rmTags <Tag:Type[;Tag:Type]*>] [--noeof] [--params] |
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| = Parameters = | | = Parameters = |
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| </pre> | | </pre> |
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− | = Usage =
| + | |
− | ./bam squeeze --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <refFilePath/Name>] [--keepOQ] [--keepDups] [--readName <readNameMapFile.txt>] [--sReadName <readNameMapFile.txt>] [--binQualS <minQualBin2>,<minQualBin3><...>] [--binQualF <filename>] [--rmTags <Tag:Type[;Tag:Type]*>] [--noeof] [--params]
| + | {{inBAMInputFile}} |
| + | {{outBAMOutputFile}} |
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