BamUtil: writeRegion - Revision history

Mktrost at 16:30, 6 January 2014

2014-01-06T16:30:44Z

← Older revision		Revision as of 16:30, 6 January 2014
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	Use <code>--excludeFlags</code> followed by the flags (as one integer) to skip any records that has any of the specified flags set.		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>) ===		=== 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.		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}}		{{paramsParameter}}

Mktrost: /* Skip an Records with any of the Specified Flags (--excludeFlags) */

2014-01-06T13:54:02Z

Skip an Records with any of the Specified Flags (--excludeFlags)

← Older revision		Revision as of 13:54, 6 January 2014
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	Left shift indels as far as they can go in the read.		Left shift indels as far as they can go in the read.

	=== Skip an Records with any of the Specified Flags (<code>--excludeFlags</code>) ===		=== 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.		Use <code>--excludeFlags</code> followed by the flags (as one integer) to skip any records that has any of the specified flags set.

Mktrost at 22:19, 3 January 2014

2014-01-03T22:19:43Z

← Older revision		Revision as of 22:19, 3 January 2014
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	== Optional Region Specifying Parameters ==		== Optional Region Specifying Parameters ==
	{{bamIndex~~\|hdr====~~}}		{{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 <code>--refName</code> followed by the reference name or </code>--refID</code> followed by the reference id.		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.

Mktrost at 22:15, 3 January 2014

2014-01-03T22:15:45Z

← Older revision		Revision as of 22:15, 3 January 2014
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	Use <code>--requiredFlags</code> followed by the flags (as one integer) to only process records with all of the specified flags set.		Use <code>--requiredFlags</code> followed by the flags (as one integer) to only process records with all of the specified flags set.

	{{paramsParameter~~\|hdr====~~}}		{{paramsParameter}}
	{{noeofBGZFParameter~~\|hdr====~~}}		{{noeofBGZFParameter}}
	{{PhoneHomeParameters}}		{{PhoneHomeParameters}}

Mktrost at 22:07, 3 January 2014

2014-01-03T22:07:32Z

← Older revision		Revision as of 22:07, 3 January 2014
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	</pre>		</pre>
	{{PhoneHomeParamDesc}}		{{PhoneHomeParamDesc}}

			== Required Parameters ==
	{{InBAMInputFile}}		{{InBAMInputFile}}
	{{OutBAMOutputFile}}		{{OutBAMOutputFile}}

Mktrost: /* Optional Parameters For Other Operations */

2014-01-03T21:32:22Z

Optional Parameters For Other Operations

← Older revision		Revision as of 21:32, 3 January 2014
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	Left shift indels as far as they can go in the read.		Left shift indels as far as they can go in the read.

			=== Skip an 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.

			=== 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.

	{{paramsParameter\|hdr====}}		{{paramsParameter\|hdr====}}

Mktrost at 21:29, 3 January 2014

2014-01-03T21:29:05Z

← Older revision		Revision as of 21:29, 3 January 2014
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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.
	</pre>		</pre>
			{{PhoneHomeParamDesc}}
	{{InBAMInputFile}}		{{InBAMInputFile}}
	{{OutBAMOutputFile}}		{{OutBAMOutputFile}}
	~~{{bamIndex}}~~

	== Region Specifying Parameters ==		== Optional Region Specifying Parameters ==
			{{bamIndex\|hdr====}}
	=== 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>.
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	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 in the CIGAR (<code>--lshift</code>) ===

	Left shift indels as far as they can go in the read.		Left shift indels as far as they can go in the read.

	{{~~noeofBGZFParameter~~}}		{{paramsParameter\|hdr====}}
	{{~~paramsParameter~~}}		{{noeofBGZFParameter\|hdr====}}
	{{PhoneHomeParameters}}		{{PhoneHomeParameters}}

Mktrost at 20:27, 3 January 2014

2014-01-03T20:27:40Z

← Older revision		Revision as of 20:27, 3 January 2014
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	{{noeofBGZFParameter}}		{{noeofBGZFParameter}}
	{{paramsParameter}}		{{paramsParameter}}
			{{PhoneHomeParameters}}

	= Return Value =		= Return Value =

Mktrost at 17:12, 6 March 2012

2012-03-06T17:12:25Z

← Older revision		Revision as of 17:12, 6 March 2012
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	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.

Mktrost at 17:12, 6 March 2012

2012-03-06T17:12:06Z

@@ Line 10: / Line 10: @@
 ** overlapping or fully within if <code>--withinReg</code> is specified
 * have a specific read name (if specified)
@@ Line 17: / Line 22: @@
 		--in        : the BAM file to be read
 		--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
 		              (if not specified, uses the --in value + ".bai")
@@ Line 36: / Line 41: @@
 		--withinReg : only print reads fully enclosed within the region.
 		--readName  : only print reads with this read name.
 		--params    : print the parameter settings
 		--noeof     : do not expect an EOF block on a bam file.
 </pre>
-= Usage =
+{{InBAMInputFile}}
 = Return Value =
 *     0: all records are successfully read and written.