Changes

</pre>

</pre>

{{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}}

{{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.