3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
= Overview of the <code>dumpAsp</code> function of <code>bamUtil</code> =
= Overview of the <code>dumpAsp</code> function of <code>bamUtil</code> =
The <code>dumpAsp</code> option on the [[bamUtil]] executable prints the contents of an ASP file in a readable format to stdout.
The <code>dumpAsp</code> option on the [[bamUtil]] executable prints the contents of an [[LibStatGen: ASP|ASP]] file in a readable format to stdout.
<span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>
</pre>
</pre>
== Asp File Name <code>(--asp)</code>==
== Required Parameters ==
=== Asp File Name <code>(--asp)</code>===
Use <code>--asp</code> followed by the file name of the ASP file that you want to read.
Use <code>--asp</code> followed by the file name of the ASP file that you want to read.
== Only print Data Records <code>(--dataOnly)</code>==
This option accepts both gzipped files and uncompressed files.
== Optional Parameters ==
=== Only print Data Records <code>(--dataOnly)</code>===
The <code>--dataOnly</code> option tells the tool to print only Reference Only and Detailed records. Any Empty and Position records are not printed.
The <code>--dataOnly</code> option tells the tool to print only Reference Only and Detailed records. Any Empty and Position records are not printed.
<code>DETAILED</code> records have 6 additional fields:
<code>DETAILED</code> records have 6 additional fields:
# numBases - the number of bases at this position
# numBases - the number of bases at this position
# bases - the bases at this position. String of ACTGND characters that is numBases long. ('D' represents a deletion.)
# bases - the bases at this position. String of ACTGND characters that is numBases long. ('D' represents a deletion)
# qualities - the qualities at this position. String of characters representing the qualities that is numBases long. (' ' represents the quality of a deletion)
# qualities - the qualities at this position. String of characters representing the qualities that is numBases long. (' ' represents the quality of a deletion)
# cycles - the cycles for this position. There are numBases cycles, separated by a ':'.
# cycles - the cycles for this position. There are numBases cycles, separated by a ':'. (-1 represents the cycle of a deletion)
# strands - the strands for this position. Sequence of numBases 0's and 1's. 0 represents forward strand and 1 represents reverse strand.
# strands - the strands for this position. Sequence of numBases 0's and 1's. 0 represents forward strand and 1 represents reverse strand.
# mqs - the mapping qualities for this position. There are numBases mapping qualities, separated by a ':'.
# mqs - the mapping qualities for this position. There are numBases mapping qualities, separated by a ':'.
