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--ignoreStrand : ignore strand information - do not reverse left/right for reverse reads
--ignoreStrand : ignore strand information - do not reverse left/right for reverse reads
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== Required Parameters==
=== Input File (1st argument) ===
The first argument is the name of the SAM/BAM input file.
The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.
A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).
{|border="1" cellspacing="0" cellpadding="2"
|SAM/BAM/Uncompressed BAM from file
| <code>yourFileName</code>
|-
|SAM from stdin
| <code>-</code>
|-
|BAM from stdin
| <code>-.bam</code>
|-
|Uncompressed BAM from stdin
| <code>-.ubam</code>
|}
Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported.
=== output File (2nd argument) ===
The second argument is the name of the SAM/BAM output file.
The file extension is used to determine whether to write SAM/BAM/uncompressed BAM. A <code>-</code> is used to indicate stdout and the extension for file type (no extension is SAM).
{|border="1" cellspacing="0" cellpadding="2"
|SAM to file
| <code>yourFileName.sam</code>
|-
|BAM to file
| <code>yourFileName.bam</code>
|-
|Uncompressed BAM to file
| <code>yourFileName.ubam</code>
|-
|SAM to stdout
| <code>-</code>
|-
|BAM to stdout
| <code>-.bam</code>
|-
|Uncompressed BAM to stdout
| <code>-.ubam</code>
|}
Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported.
==Optional parameters==
=== Number of Bases to Trim from Each End (3rd argument) ===
If the 3rd argument a number (with no flag/option), it is the number of bases to trim from each end of the reads.
===Trim Bases from the Left (<code>--left</code> or <code>--L</code>)===
Use <code>--left</code> or <code>--L</code> followed by the number of bases to be trimmed from the left.
By default reverse strands are reversed and then the left is trimmed, meaning that <code>--left</code> actually trims from the right of the read in the SAM/BAM for reverse reads.
Use [[Ignore the Strand when Trimming (--ignoreStrand or --i)|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.
===Trim Bases from the Right (<code>--right</code> or <code>--R</code>)===
Use <code>--right</code> or <code>--R</code> followed by the number of bases to be trimmed from the right.
By default reverse strands are reversed and then the right is trimmed, meaning that <code>--right</code> actually trims from the left of the read in the SAM/BAM for reverse reads.
Use [[Ignore the Strand when Trimming (--ignoreStrand or --i)|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.
=== Ignore the Strand when Trimming (<code>--ignoreStrand</code> or <code>--i</code>) ===
Use <code>--ignoreStrand</code> or <code>--i</code> to ignore the strand information and treat forward/reverese the same. When <code>--ignoreStrand</code> or <code>--i</code> is set, do not reverse reverse reads prior to trimming left/right.
{{noeofBGZFParameter}}
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
Returns the SamStatus for the reads/writes. 0 on success.
Returns the SamStatus for the reads/writes. 0 on success, non-0 on failure.
= Examples =
= Examples =
