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** overlapping or fully within if <code>--withinReg</code> is specified
** overlapping or fully within if <code>--withinReg</code> is specified
* have a specific read name (if specified)
* have a specific read name (if specified)
= Usage =
./bam writeRegion --in <inputFilename> --out <outputFilename> [--bamIndex <bamIndexFile>] [--refName <reference Name> | --refID <reference ID>] [--start <0-based start pos>] [--end <0-based end psoition>] [--bed <bed filename>] [--withinRegion] [--readName <readName>] [--lshift] [--params] [--noeof]
--in : the BAM file to be read
--in : the BAM file to be read
--out : the SAM/BAM file to write to
--out : the SAM/BAM file to write to
Optional Parameters:
Optional Parameters for Specifying a Region:
--bamIndex : the path/name of the bam index file
--bamIndex : the path/name of the bam index file
(if not specified, uses the --in value + ".bai")
(if not specified, uses the --in value + ".bai")
--withinReg : only print reads fully enclosed within the region.
--withinReg : only print reads fully enclosed within the region.
--readName : only print reads with this read name.
--readName : only print reads with this read name.
--params : print the parameter settings
Optional Parameters For Other Operations:
--noeof : do not expect an EOF block on a bam file.
--lshift : left shift indels when writing records
--excludeFlags : Skip any records with any of the specified flags set
(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}}
{{OutBAMOutputFile}}
== Optional Region Specifying Parameters ==
{{bamIndex}}
=== 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 <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>.
The reference Name is the name specified in the <code>RNAME</code> field of the records in the SAM file or in the <code>name</code> fields of the reference information section of the BAM file.
The reference ID is the value specified in the <code>refID</code> field of the records in the BAM file.
If you want to read only unmapped reads, use <code>--refID -1</code>
=== Read only a Specific Region of a Chromosome (<code>--start</code> and <code>--end</code>) ===
You can only specify a specific region if you also specify a specific reference/chromosome using <code>--refName</code> or <code>--refID</code>.
Use <code>--start</code> to specify the inclusive 0-based start position of the region you want to read. Specify <code>--start -1</code> to specify start at the beginning of the specified chromosome.
Use <code>--end</code> to specify the exclusive 0-based end position of the region you want to read. Specify <code>--end -1</code> to specify end of the specified chromosome.
=== Bed File with Regions to Write (<code>--bed</code>) ===
If <code>--bed</code> followed by a filename is specified the regions specified in the bed file will be written.
It is assumed that the regions in the bed file are sorted.
=== Only Write Reads Fully within the Specified Region (<code>--withinReg</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.
=== 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.
== Optional Parameters For Other Operations ==
=== Left Shift Indels in the CIGAR (<code>--lshift</code>) ===
= Usage =
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.
=== 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}}
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
* 0: all records are successfully read and written.
* 0: all records are successfully read and written.
