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| = Parameters = | | = Parameters = |
− | <pre> Required Parameters: | + | <pre> Required Parameters: |
− | --in : the SAM/BAM file to be read
| + | --in : the SAM/BAM file to be read |
− | --out : the SAM/BAM file to be written
| + | --out : the SAM/BAM file to be written |
− | Optional Parameters:
| + | Optional Parameters: |
− | --refFile : reference file name
| + | --refFile : reference file name |
− | --lshift : left shift indels when writing records
| + | --lshift : left shift indels when writing records |
− | --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 |
− | --recover : attempt to recover the input bam file
| + | --recover : attempt error recovery while reading a bam file |
− | Optional Sequence Parameters (only specify one):
| + | Optional Sequence Parameters (only specify one): |
− | --seqOrig : Leave the sequence as is (default & used if reference is not specified)
| + | --useOrigSeq : Leave the sequence as is (default & used if reference is not specified) |
− | --seqBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --ref)
| + | --useBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --refFile) |
− | --seqEquals : Convert any bases that match the reference to '=' (requires --ref)
| + | --useEquals : Convert any bases that match the reference to '=' (requires --refFile) |
| </pre> | | </pre> |
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| See [[#BAM File Recovery |BAM File Recovery]]. | | See [[#BAM File Recovery |BAM File Recovery]]. |
| | | |
− | == Sequence Representation Parameters (<code>--seqOrig</code>, <code>--seqBases</code>, <code>--seqEquals</code>, <code>--refFile</code>) == | + | == Sequence Representation Parameters (<code>--useOrigSeq</code>, <code>--useBases</code>, <code>--useEquals</code>, <code>--refFile</code>) == |
| | | |
| The sequence parameters options specify how to represent the sequence if the reference is specified (refFile option). | | The sequence parameters options specify how to represent the sequence if the reference is specified (refFile option). |
| | | |
− | If the reference is not specified or seqOrig is specified, no modifications are made to the sequence. | + | If the reference is not specified or useOrigSeq is specified, no modifications are made to the sequence. |
| | | |
− | If the reference and seqBases is specified, any matches between the sequence and the reference are represented in the sequence as the appropriate base. | + | If the reference and useBases is specified, any matches between the sequence and the reference are represented in the sequence as the appropriate base. |
| | | |
− | If the reference and seqEquals is specified, any matches between the sequence and the reference are represented in the sequence as '='. | + | If the reference and useEquals is specified, any matches between the sequence and the reference are represented in the sequence as '='. |
| | | |
| === Examples === | | === Examples === |
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| Sequence with Equals: AA======G===GGG | | Sequence with Equals: AA======G===GGG |
| | | |
| + | {{PhoneHomeParameters}} |
| | | |
| = BAM File Recovery = | | = BAM File Recovery = |