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--readName : only print reads with this read name.
--readName : only print reads with this read name.
Optional Parameters For Other Operations:
Optional Parameters For Other Operations:
--lshift : left shift indels when writing records
--lshift : left shift indels when writing records
--params : print the parameter settings
--excludeFlags : Skip any records with any of the specified flags set
--noeof : do not expect an EOF block on a bam file.
(specify an integer representation of the flags)
--requiredFlags : Only process records with all of the specified flags set
(specify an integer representation of the flags)
--params : print the parameter settings
--noeof : do not expect an EOF block on a bam file.
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{{PhoneHomeParamDesc}}
== Required Parameters ==
{{InBAMInputFile}}
{{InBAMInputFile}}
{{OutBAMOutputFile}}
{{OutBAMOutputFile}}
== Optional Region Specifying Parameters ==
{{bamIndex}}
{{bamIndex}}
=== Read only a Specific Reference/Chromosome (<code>--refName</code> or <code>--refID</code>) ===
=== Read only a Specific Reference/Chromosome (<code>--refName</code> or <code>--refID</code>) ===
If you only want to read a specific reference (chromosome), specify either the reference name following <code>--refName</code> or the reference id following </code>--refID</code>.
If you only want to read a specific reference (chromosome), specify either <code>--refName</code> followed by the reference name or </code>--refID</code> followed by the reference id.
If you want to read all references, don't specify either <code>--refName</code> or <code>--refID</code>.
If you want to read all references, don't specify either <code>--refName</code> or <code>--refID</code>.
By default reads that overlap the specified region are written. If instead you only want to write reads that are fully within the specified regions, use the <code>--withinReg</code> option.
By default reads that overlap the specified region are written. If instead you only want to write reads that are fully within the specified regions, use the <code>--withinReg</code> option.
=== Only Print Reads with a Specified Read Name (code>--readName</code>) ===
=== Only Print Reads with a Specified Read Name (<code>--readName</code>) ===
If you only want to print reads with a specific read name, use the <code>--readName</code> option followed by the read name.
If you only want to print reads with a specific read name, use the <code>--readName</code> option followed by the read name.
== Optional Parameters For Other Operations ==
=== Left Shift Indels in the CIGAR (<code>--lshift</code>) ===
Left shift indels as far as they can go in the read.
=== Skip Records with any of the Specified Flags (<code>--excludeFlags</code>) ===
Use <code>--excludeFlags</code> followed by the flags (as one integer) to skip any records that has any of the specified flags set.
This parameter was added in version 1.0.10.
== Left Shift Indels in the CIGAR (<code>--lshift</code>) ==
=== Only Process Records with the all of the Specified Flags (<code>--requiredFlags</code>) ===
Use <code>--requiredFlags</code> followed by the flags (as one integer) to only process records with all of the specified flags set.
This parameter was added in version 1.0.10.
{{paramsParameter}}
{{noeofBGZFParameter}}
{{noeofBGZFParameter}}
{{paramsParameter}}
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
