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[[Category:BamUtil|findCigars]]
[[Category:BAM Software]]
[[Category:Software]]
= Overview of the <code>findCigars</code> function of <code>bamUtil</code> =
The <code>findCigars</code> option on the [[bamUtil]] executable outputs just the reads that contain any of the specified CIGAR operations.
= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
--out : the SAM/BAM file to be written
Optional Parameters:
--cinsert : output reads that contain insertions ('I').
--cdel : output reads that contain deletions ('D').
--cpad : output reads that contain pads ('P').
--cskip : output reads that contain skips ('N').
--chardClip : output reads that contain hard clips ('H').
--csoftClip : output reads that contain soft clips ('S').
--nonM : output reads that contain any non match/mismatch (anything other than 'M', '=', 'X')
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
</pre>
= Usage =
./bam findCigars --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--cinsert] [--cdel] [--cpad] [--cskip] [--chardClip] [--csoftClip] [--nonM] [--noeof] [--params]
= Return Value =
Returns the SamStatus for the reads/writes.
= Example Output =
<pre>
Number of records read = 10
Number of records written = 1
</pre>
[[Category:BAM Software]]
[[Category:Software]]
= Overview of the <code>findCigars</code> function of <code>bamUtil</code> =
The <code>findCigars</code> option on the [[bamUtil]] executable outputs just the reads that contain any of the specified CIGAR operations.
= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
--out : the SAM/BAM file to be written
Optional Parameters:
--cinsert : output reads that contain insertions ('I').
--cdel : output reads that contain deletions ('D').
--cpad : output reads that contain pads ('P').
--cskip : output reads that contain skips ('N').
--chardClip : output reads that contain hard clips ('H').
--csoftClip : output reads that contain soft clips ('S').
--nonM : output reads that contain any non match/mismatch (anything other than 'M', '=', 'X')
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
</pre>
= Usage =
./bam findCigars --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--cinsert] [--cdel] [--cpad] [--cskip] [--chardClip] [--csoftClip] [--nonM] [--noeof] [--params]
= Return Value =
Returns the SamStatus for the reads/writes.
= Example Output =
<pre>
Number of records read = 10
Number of records written = 1
</pre>
