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[[Category:BamUtil|clipOverlap]]
[[Category:BAM Software]]
[[Category:Software]]
= Overview of the <code>clipOverlap</code> function of <code>bamUtil</code> =
The <code>clipOverlap</code> option on the [[bamUtil]] executable clips overlapping read pairs.
'''RESTRICTIONS'''
This tool assumes the file is sorted by ReadName.
= Rules for Clipping =
== Clipping from the front==
The first operation after the softclip will be a Match/Mismatch, meaning that any trailing pads, deletions, insertions, or skips will also be soft clipped.
{|border="1" cellspacing="0" cellpadding="2"
! Clip Location !! How it is handled
|-
|If the clip position falls in a skip/deletion
| Removes the entire skip/deletion
|-
|If the position immediately after the clip is a skip/deletion
| Also removes the skip/deletion
|-
|If the position immediately after the clip is an Insert
| Softclips the insert
|-
|If the position immediately after the clip is a Pad
| Removes the pad
|-
| Last match/mismatch position of the read (the entire read is clipped)
| Entire read is soft clipped, 0-based position changed left as the original (not modified)
|}
== Clipping from the back==
{|border="1" cellspacing="0" cellpadding="2"
! Clip Location !! How it is handled
|-
|}
= Usage =
= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
--out : the SAM/BAM file to be written
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
</pre>
{{inBAMInputFile}}
{{outBAMOutputFile}}
= Return Value =
Returns the SamStatus for the reads/writes.
= Example Output =
<pre>
</pre>
[[Category:BAM Software]]
[[Category:Software]]
= Overview of the <code>clipOverlap</code> function of <code>bamUtil</code> =
The <code>clipOverlap</code> option on the [[bamUtil]] executable clips overlapping read pairs.
'''RESTRICTIONS'''
This tool assumes the file is sorted by ReadName.
= Rules for Clipping =
== Clipping from the front==
The first operation after the softclip will be a Match/Mismatch, meaning that any trailing pads, deletions, insertions, or skips will also be soft clipped.
{|border="1" cellspacing="0" cellpadding="2"
! Clip Location !! How it is handled
|-
|If the clip position falls in a skip/deletion
| Removes the entire skip/deletion
|-
|If the position immediately after the clip is a skip/deletion
| Also removes the skip/deletion
|-
|If the position immediately after the clip is an Insert
| Softclips the insert
|-
|If the position immediately after the clip is a Pad
| Removes the pad
|-
| Last match/mismatch position of the read (the entire read is clipped)
| Entire read is soft clipped, 0-based position changed left as the original (not modified)
|}
== Clipping from the back==
{|border="1" cellspacing="0" cellpadding="2"
! Clip Location !! How it is handled
|-
|}
= Usage =
= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
--out : the SAM/BAM file to be written
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
</pre>
{{inBAMInputFile}}
{{outBAMOutputFile}}
= Return Value =
Returns the SamStatus for the reads/writes.
= Example Output =
<pre>
</pre>
