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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]
= Parameters =
= Parameters =
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{{inBAMInputFile}}
{{outBAMOutputFile}}
