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, 17:08, 27 January 2012
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| | {{paramsParameter}} | | {{paramsParameter}} |
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| − | == Asp File Name <code>(--asp)</code>==
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| − | Use <code>--asp</code> followed by the file name of the ASP file that you want to read.
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| − | == Only print Data Records <code>(--dataOnly)</code>==
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| − | The <code>--dataOnly</code> option tells the tool to print only Reference Only and Detailed records. Any Empty and Position records are not printed.
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| − | {{paramsParameter}}
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| | = Return Value = | | = Return Value = |
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| | =Output= | | =Output= |
| − | Each ASP record is printed on one line with each field separated by a <code>tab</code>.
| + | An [[LibStatGen: ASP|ASP]] file is written containing the pileup for the specified BAM file. |
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| − | The 1st field in the row is the chromosomeID and 0-based position separated by a ':'.
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| − | The 2nd field is the record type, <code>POS</code>, <code>EMPTY</code>, <code>REF_ONLY</code>, or <code>DETAILED</code>.
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| − | <code>POS</code> and <code>EMPTY</code> records have no additional columns.
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| − | <code>REF_ONLY</code> records have 3 additional fields:
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| − | # numBases - the number of bases at this position
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| − | # GLH - the GLH for this position
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| − | # GLA - the GLA for this position
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| − | <code>DETAILED</code> records have 6 additional fields:
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| − | # numBases - the number of bases at this position
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| − | # bases - the bases at this position. String of ACTGND characters that is numBases long. ('D' represents a deletion)
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| − | # qualities - the qualities at this position. String of characters representing the qualities that is numBases long. (' ' represents the quality of a deletion)
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| − | # cycles - the cycles for this position. There are numBases cycles, separated by a ':'. (-1 represents the cycle of a deletion)
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| − | # strands - the strands for this position. Sequence of numBases 0's and 1's. 0 represents forward strand and 1 represents reverse strand.
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| − | # mqs - the mapping qualities for this position. There are numBases mapping qualities, separated by a ':'.
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| − | ==Sample Output==
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