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<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>
<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>
== Rules ==
'''Dealing with 'N' Bases'''
* If the reference is 'N':
** Do Not write REF_ONLY or DETAILED records
** Either write EMPTY or no record (depending on Gap Size and the next data record)
* If all reads at this position are 'N':
** Either write EMPTY or no record (depending on Gap Size and the next data record)
* If some reads are 'N' and the rest are the reference (not 'N')
** Write a REF_ONLY record but do not include the 'N's in the numBases
* If some reads are 'N' and some are non-reference (not 'N')
** DEFAULT: Write a DETAILED record and include the 'N's in the numBases
** OPTIONAL: Write a DETAILED record but do not include the 'N's in the numBases
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== Required Parameters ==
{{inBAMInputFile}}
{{inBAMInputFile}}
== output File <code>(--out)</code>==
=== output File <code>(--out)</code>===
Use <code>--out</code> followed by your file name to specify the ASP file to write from the pileup.
Use <code>--out</code> followed by your file name to specify the ASP file to write from the pileup.
{{RefFile}}
{{RefFile}}
== Optional Parameters ==
{{BamIndex}}
{{BamIndex}}
== Region List <code>(--regionList)</code> ==
=== Region List <code>(--regionList)</code> ===
Use the <code>--regionList</code> option if you only want to pileup specific regions instead of the entire BAM file. The region list file has one region on each line.
Use the <code>--regionList</code> option if you only want to pileup specific regions instead of the entire BAM file. The region list file has one region on each line.
If a position is covered by multiple regions, the position will be piled up multiple times (once for each region).
If a position is covered by multiple regions, the position will be piled up multiple times (once for each region).
== Gap Size <code>(--gapSize)</code> ==
=== Gap Size <code>(--gapSize)</code> ===
When writing an ASP file, there are two ways to skip positions that do not have any data (records/bases) associated with them.
When writing an ASP file, there are two ways to skip positions that do not have any data (records/bases) associated with them.
# Write an Empty record indicating no data for that position.
# Write an Empty record indicating no data for that position.
=Output=
=Output=
An [[LibStatGen: ASP|ASP]] file is written containing the pileup for the specified BAM file.
An [[LibStatGen: ASP|ASP]] file is written containing the pileup for the specified BAM file. ASP files are by default compressed using BGZF.
The number of each type of record is output to stderr.
For example:
<pre>
Number of Position Records = 6
Number of Empty Records = 39
Number of Reference Only Records = 12
Number of Detailed Records = 29
</pre>
