BamUtil: convert - Revision history

Mktrost: /* Return Value */

2014-01-03T22:27:37Z

Return Value

← Older revision		Revision as of 22:27, 3 January 2014
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	= Return Value =		= Return Value =

	Returns the SamStatus for the reads/writes (0 is success).		Returns the SamStatus for the reads/writes (0 for success, non-0 for failure).

	= Example Output =		= Example Output =

Mktrost at 21:42, 3 January 2014

2014-01-03T21:42:00Z

← Older revision		Revision as of 21:42, 3 January 2014
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	{{PhoneHomeParamDesc}}		{{PhoneHomeParamDesc}}

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

			== Optional Parameters ==
	{{refFile}}		{{refFile}}

	== 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.
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	{{paramsParameter}}		{{paramsParameter}}

	== Recover a corrupted BAM file (<code>--recover</code>) ==		=== Recover a corrupted BAM file (<code>--recover</code>) ===

	See [[#BAM File Recovery \|BAM File Recovery]].		See [[#BAM File Recovery \|BAM File Recovery]].

Mktrost: /* Parameters */

2014-01-03T20:45:26Z

Parameters

← Older revision		Revision as of 20:45, 3 January 2014
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	--useBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --refFile)		--useBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --refFile)
	--useEquals : Convert any bases that match the reference to '=' (requires --refFile)		--useEquals : Convert any bases that match the reference to '=' (requires --refFile)
	~~PhoneHome:~~
	~~--noPhoneHome : disable PhoneHome (default enabled)~~
	~~--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)~~
	</pre>		</pre>
			{{PhoneHomeParamDesc}}

	{{InBAMInputFile}}		{{InBAMInputFile}}
	{{OutBAMOutputFile}}		{{OutBAMOutputFile}}

Mktrost: /* Parameters */

2014-01-03T20:42:52Z

Parameters

← Older revision		Revision as of 20:42, 3 January 2014
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	--useBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --refFile)		--useBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --refFile)
	--useEquals : Convert any bases that match the reference to '=' (requires --refFile)		--useEquals : Convert any bases that match the reference to '=' (requires --refFile)
	~~</pre>~~		PhoneHome:
	~~<pre>~~ PhoneHome:
	--noPhoneHome : disable PhoneHome (default enabled)		--noPhoneHome : disable PhoneHome (default enabled)
	--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)		--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)

Mktrost: /* Parameters */

2014-01-03T20:41:52Z

Parameters

← Older revision		Revision as of 20:41, 3 January 2014
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	</pre>		</pre>
	<pre> PhoneHome:		<pre> PhoneHome:
	--noPhoneHome : disable PhoneHome (default ~~disabled~~)		--noPhoneHome : disable PhoneHome (default enabled)
	--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)		--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)
	</pre>		</pre>

Mktrost: /* Parameters */

2014-01-03T20:41:40Z

Parameters

← Older revision		Revision as of 20:41, 3 January 2014
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	--noPhoneHome : disable PhoneHome (default disabled)		--noPhoneHome : disable PhoneHome (default disabled)
	--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)		--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)
	~~Optional Parameters:~~
	</pre>		</pre>
	{{InBAMInputFile}}		{{InBAMInputFile}}

Mktrost: /* Parameters */

2014-01-03T20:41:21Z

Parameters

← Older revision		Revision as of 20:41, 3 January 2014
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	--useEquals : Convert any bases that match the reference to '=' (requires --refFile)		--useEquals : Convert any bases that match the reference to '=' (requires --refFile)
	</pre>		</pre>
			<pre> PhoneHome:
			--noPhoneHome : disable PhoneHome (default disabled)
			--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)
			Optional Parameters:
			</pre>
	{{InBAMInputFile}}		{{InBAMInputFile}}
	{{OutBAMOutputFile}}		{{OutBAMOutputFile}}

Mktrost at 20:26, 3 January 2014

2014-01-03T20:26:30Z

← Older revision		Revision as of 20:26, 3 January 2014
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	= Parameters =		= Parameters =
	<pre> Required Parameters:		<pre> Required Parameters:
	--in ~~ ~~: the SAM/BAM file to be read		--in : the SAM/BAM file to be read
	--out ~~ ~~: the SAM/BAM file to be written		--out : the SAM/BAM file to be written
	Optional Parameters:		Optional Parameters:
	--refFile ~~ ~~: reference file name		--refFile : reference file name
	--lshift ~~ ~~: left shift indels when writing records		--lshift : left shift indels when writing records
	--noeof ~~ ~~: do not expect an EOF block on a bam file		--noeof : do not expect an EOF block on a bam file
	--params ~~ ~~: print the parameter settings		--params : print the parameter settings
	--recover ~~ ~~: attempt ~~to recover the input~~ bam file		--recover : attempt error recovery while reading a bam file
	Optional Sequence Parameters (only specify one):		Optional Sequence Parameters (only specify one):
	--~~seqOrig  ~~: Leave the sequence as is (default &~~amp;~~ used if reference is not specified)		--useOrigSeq : Leave the sequence as is (default & used if reference is not specified)
	--~~seqBases  ~~: Convert any '=' in the sequence to the appropriate base using the reference (requires --~~ref~~)		--useBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --refFile)
	--~~seqEquals ~~: Convert any bases that match the reference to '=' (requires --~~ref~~)		--useEquals : Convert any bases that match the reference to '=' (requires --refFile)
	</pre>		</pre>

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	See [[#BAM File Recovery \|BAM File Recovery]].		See [[#BAM File Recovery \|BAM File Recovery]].

	== Sequence Representation Parameters (<code>--~~seqOrig~~</code>, <code>--~~seqBases~~</code>, <code>--~~seqEquals~~</code>, <code>--refFile</code>) ==		== Sequence Representation Parameters (<code>--useOrigSeq</code>, <code>--useBases</code>, <code>--useEquals</code>, <code>--refFile</code>) ==

	The sequence parameters options specify how to represent the sequence if the reference is specified (refFile option).		The sequence parameters options specify how to represent the sequence if the reference is specified (refFile option).

	If the reference is not specified or ~~seqOrig~~ is specified, no modifications are made to the sequence.		If the reference is not specified or useOrigSeq is specified, no modifications are made to the sequence.

	If the reference and ~~seqBases~~ is specified, any matches between the sequence and the reference are represented in the sequence as the appropriate base.		If the reference and useBases is specified, any matches between the sequence and the reference are represented in the sequence as the appropriate base.

	If the reference and ~~seqEquals~~ is specified, any matches between the sequence and the reference are represented in the sequence as '='.		If the reference and useEquals is specified, any matches between the sequence and the reference are represented in the sequence as '='.

	=== Examples ===		=== Examples ===
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	Sequence with Equals: AA======G===GGG		Sequence with Equals: AA======G===GGG

			{{PhoneHomeParameters}}

	= BAM File Recovery =		= BAM File Recovery =

Mktrost: /* Return Value */

2014-01-03T19:06:13Z

Return Value

← Older revision		Revision as of 19:06, 3 January 2014
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	= Return Value =		= Return Value =

	Returns the SamStatus for the reads/writes.		Returns the SamStatus for the reads/writes (0 is success).

	= Example Output =		= Example Output =

Mktrost at 15:57, 6 March 2012

2012-03-06T15:57:23Z

← Older revision		Revision as of 15:57, 6 March 2012
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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.


	{{noeofBGZFParameter}}		{{noeofBGZFParameter}}
	{{paramsParameter}}		{{paramsParameter}}


	== Recover a corrupted BAM file (<code>--recover</code>) ==		== Recover a corrupted BAM file (<code>--recover</code>) ==

	See [[#BAM File Recovery \|BAM File Recovery]].		See [[#BAM File Recovery \|BAM File Recovery]].


	== Sequence Representation Parameters (<code>--seqOrig</code>, <code>--seqBases</code>, <code>--seqEquals</code>, <code>--refFile</code>) ==		== Sequence Representation Parameters (<code>--seqOrig</code>, <code>--seqBases</code>, <code>--seqEquals</code>, <code>--refFile</code>) ==