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407 bytes added
, 17:29, 3 January 2014
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| --readName : only print reads with this read name. | | --readName : only print reads with this read name. |
| Optional Parameters For Other Operations: | | Optional Parameters For Other Operations: |
− | --lshift : left shift indels when writing records | + | --lshift : left shift indels when writing records |
− | --params : print the parameter settings | + | --excludeFlags : Skip any records with any of the specified flags set |
− | --noeof : do not expect an EOF block on a bam file. | + | (specify an integer representation of the flags) |
| + | --requiredFlags : Only process records with all of the specified flags set |
| + | (specify an integer representation of the flags) |
| + | --params : print the parameter settings |
| + | --noeof : do not expect an EOF block on a bam file. |
| </pre> | | </pre> |
− | | + | {{PhoneHomeParamDesc}} |
| {{InBAMInputFile}} | | {{InBAMInputFile}} |
| {{OutBAMOutputFile}} | | {{OutBAMOutputFile}} |
− | {{bamIndex}}
| |
| | | |
− | == Region Specifying Parameters == | + | == Optional Region Specifying Parameters == |
| + | {{bamIndex|hdr====}} |
| === Read only a Specific Reference/Chromosome (<code>--refName</code> or <code>--refID</code>) === | | === Read only a Specific Reference/Chromosome (<code>--refName</code> or <code>--refID</code>) === |
− | If you only want to read a specific reference (chromosome), specify either the reference name following <code>--refName</code> or the reference id following </code>--refID</code>. | + | If you only want to read a specific reference (chromosome), specify either <code>--refName</code> followed by the reference name or </code>--refID</code> followed by the reference id. |
| | | |
| If you want to read all references, don't specify either <code>--refName</code> or <code>--refID</code>. | | If you want to read all references, don't specify either <code>--refName</code> or <code>--refID</code>. |
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| If you only want to print reads with a specific read name, use the <code>--readName</code> option followed by the read name. | | If you only want to print reads with a specific read name, use the <code>--readName</code> option followed by the read name. |
| | | |
− | | + | == Optional Parameters For Other Operations == |
− | == Left Shift Indels in the CIGAR (<code>--lshift</code>) == | + | === Left Shift Indels in the CIGAR (<code>--lshift</code>) === |
| | | |
| Left shift indels as far as they can go in the read. | | Left shift indels as far as they can go in the read. |
| | | |
− | {{noeofBGZFParameter}} | + | {{paramsParameter|hdr====}} |
− | {{paramsParameter}} | + | {{noeofBGZFParameter|hdr====}} |
| {{PhoneHomeParameters}} | | {{PhoneHomeParameters}} |
| | | |