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250 bytes added
, 11:58, 26 March 2014
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| * dropping OQ fields (default, disable using <code>--keepOQ</code>) | | * dropping OQ fields (default, disable using <code>--keepOQ</code>) |
| * dropping duplicates (default, disable using <code>--keepDups</code>) | | * dropping duplicates (default, disable using <code>--keepDups</code>) |
− | * dropping specified tags (<code>--rmTags Tag1:Type1;Tag2:Type2</code>) | + | * dropping specified tags (<code>--rmTags "Tag1:Type1;Tag2:Type2"</code>) |
| * using '=' when a base matches the reference (<code>--refFile refFileName.fa</code>) | | * using '=' when a base matches the reference (<code>--refFile refFileName.fa</code>) |
| * binning quality scores (<code>--binQualS</code><code>--binQualF</code>) | | * binning quality scores (<code>--binQualS</code><code>--binQualF</code>) |
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| = Usage = | | = 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] | + | ./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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| This version does not require the input file to have been presorted by readname, | | This version does not require the input file to have been presorted by readname, |
| but uses a lot of memory since it stores all the read names. | | but uses a lot of memory since it stores all the read names. |
− | --rmTags : Remove the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type... | + | --rmTags : Remove the specified Tags formatted as "Tag:Type;Tag:Type;Tag:Type"... |
| --noeof : do not expect an EOF block on a bam file. | | --noeof : do not expect an EOF block on a bam file. |
| --params : print the parameter settings | | --params : print the parameter settings |
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| === Remove Tags (<code>--rmTags</code>) === | | === Remove Tags (<code>--rmTags</code>) === |
− | Use <code>--rmTags</code> followed by a list of tags separated by ';' to remove the specified tags. The tags should be formatted as: <code>Tag:Type"</code> | + | Use <code>--rmTags</code> followed by a list of tags separated by ';' to remove the specified tags. The tags should be formatted as: <code>"Tag:Type"</code>. Note: when using the ';' to specify multiple tags, be sure to put the whole string in quotes - otherwise the ';' will be interpreted as the end of the command. Example: <code>--rmTags "OQ:Z;MD:Z"</code> or <code>--rmTags 'OQ:Z;MD:Z'</code> |
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| {{noeofBGZFParameter}} | | {{noeofBGZFParameter}} |