BamUtil: diff - Revision history

Mktrost: /* Optional Parmaeters */

2014-01-06T21:00:00Z

Optional Parmaeters

← Older revision		Revision as of 21:00, 6 January 2014
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	== Optional Parmaeters ==		== Optional Parmaeters ==
	=== output File (<code>--out</code>) ===		=== output File (<code>--out</code>) ===

	Use <code>--out</code> (optional) to specify the name of the output file.		Use <code>--out</code> (optional) to specify the name of the output file.

	It is output in [[Diff Format]] by default. Specify the filename with a .bam, .sam, .ubam extension to output in [[SAM/BAM Format]].		It is output in [[Diff Format]] by default. Specify the filename with a .bam, .sam, .ubam extension to output in [[SAM/BAM Format]].


	=== Fields to Diff (<code>--all</code>, <code>--flag</code>, <code>--mapQual</code>, <code>--mate</code>, <code>--isize</code>, <code>--seq</code>, <code>--baseQual</code>, <code>--tags</code>, <code>--everyTag</code>, <code>--noCigar</code>, <code>--noPos</code>, )===		=== Fields to Diff (<code>--all</code>, <code>--flag</code>, <code>--mapQual</code>, <code>--mate</code>, <code>--isize</code>, <code>--seq</code>, <code>--baseQual</code>, <code>--tags</code>, <code>--everyTag</code>, <code>--noCigar</code>, <code>--noPos</code>, )===
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	'''OR use <code>--all</code> to diff all SAM/BAM record fields.		'''OR use <code>--all</code> to diff all SAM/BAM record fields.


	=== Only print different fields (<code>--onlyDiffs</code>)===		=== Only print different fields (<code>--onlyDiffs</code>)===

	Specify <code>--onlyDiffs</code> to only print the fields that are different, otherwise for any diff all the fields that are compared are printed. The read name is always printed.		Specify <code>--onlyDiffs</code> to only print the fields that are different, otherwise for any diff all the fields that are compared are printed. The read name is always printed.


	=== Maximum Number of Records That Can be Allocated (<code>--recPoolSize</code>)===		=== Maximum Number of Records That Can be Allocated (<code>--recPoolSize</code>)===

Mktrost at 18:04, 6 January 2014

2014-01-06T18:04:28Z

← Older revision		Revision as of 18:04, 6 January 2014
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	--params : print the parameter settings		--params : print the parameter settings
	</pre>		</pre>
			{{PhoneHomeParamDesc}}

	== Required Parameters ==		== Required Parameters ==

Mktrost at 18:03, 6 January 2014

2014-01-06T18:03:49Z

← Older revision		Revision as of 18:03, 6 January 2014
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	* turn off position comparison		* turn off position comparison
	* turn off cigar comparison		* turn off cigar comparison


			= Usage =
			./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--all] [--flag] [--mapQual] [--mate] [--isize] [--seq] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--everyTag] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params]


	= Parameters =		= Parameters =
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	--onlyDiffs : only print the fields that are different, otherwise for any diff all the fields that are compared are printed.		--onlyDiffs : only print the fields that are different, otherwise for any diff all the fields that are compared are printed.
	--recPoolSize : number of records to allow to be stored at a time, default value: 1000000		--recPoolSize : number of records to allow to be stored at a time, default value: 1000000
	--posDiff : max base pair difference between possibly matching ~~records100000~~		Set to -1 for unlimited number of records
			--posDiff : max base pair difference between possibly matching records, default value: 100000
	--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
	</pre>		</pre>

	== input Files 1 & 2 (<code>--in1</code> and <code>--in2</code>) ==		== Required Parameters ==

			=== input Files 1 & 2 (<code>--in1</code> and <code>--in2</code>) ===

	Use <code>--in1</code> and <code>--in2</code> followed by your file names to specify the SAM/BAM input files to compare. They are both required.		Use <code>--in1</code> and <code>--in2</code> followed by your file names to specify the SAM/BAM input files to compare. They are both required.
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	Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported.		Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported.

			== Optional Parmaeters ==
	== output File (<code>--out</code>) ==		=== output File (<code>--out</code>) ===

	Use <code>--out</code> (optional) to specify the name of the output file.		Use <code>--out</code> (optional) to specify the name of the output file.
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	== Fields to Diff (<code>--all</code>, <code>--flag</code>, <code>--mapQual</code>, <code>--mate</code>, <code>--isize</code>, <code>--seq</code>, <code>--baseQual</code>, <code>--tags</code>, <code>--everyTag</code>, <code>--noCigar</code>, <code>--noPos</code>, )==		=== Fields to Diff (<code>--all</code>, <code>--flag</code>, <code>--mapQual</code>, <code>--mate</code>, <code>--isize</code>, <code>--seq</code>, <code>--baseQual</code>, <code>--tags</code>, <code>--everyTag</code>, <code>--noCigar</code>, <code>--noPos</code>, )===

	By default only the chromosome/position and cigar are compared for each record.		By default only the chromosome/position and cigar are compared for each record.
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	== Only print different fields (<code>--onlyDiffs</code>)==		=== Only print different fields (<code>--onlyDiffs</code>)===

	Specify <code>--onlyDiffs</code> to only print the fields that are different, otherwise for any diff all the fields that are compared are printed. The read name is always printed.		Specify <code>--onlyDiffs</code> to only print the fields that are different, otherwise for any diff all the fields that are compared are printed. The read name is always printed.


	== Maximum Number of Records That Can be Allocated (<code>--recPoolSize</code>)==		=== Maximum Number of Records That Can be Allocated (<code>--recPoolSize</code>)===
	When comparing the files, matching reads may not have the same positions and thus may not be at the same location in the files. In this case, reads need to be stored until its match is found in the other file.		When comparing the files, matching reads may not have the same positions and thus may not be at the same location in the files. In this case, reads need to be stored until its match is found in the other file.

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	When the Pool Size is exceeded, the oldest record in the file that has more records stored is released and treated as unique to that file. If the matching record is later found in the other file, it will also be treated as unique to its file. At the end of the run, a warning message is printed with the number of times the PoolSize was hit and records were forced to be released.		When the Pool Size is exceeded, the oldest record in the file that has more records stored is released and treated as unique to that file. If the matching record is later found in the other file, it will also be treated as unique to its file. At the end of the run, a warning message is printed with the number of times the PoolSize was hit and records were forced to be released.

	== Maximum Base Pair Difference Between Possibly Matching Records (<code>--posDiff</code>)==		=== Maximum Base Pair Difference Between Possibly Matching Records (<code>--posDiff</code>)===
	In order to limit th number of records that are held onto while looking for matching records, a maximum difference in position between the matches is used. This value is defaulted to 100000 amd cam be modified using <code>--posDiff</code>. Any matching pairs that are further than <code>--posDiff</code> are treated as unique to their files.		In order to limit th number of records that are held onto while looking for matching records, a maximum difference in position between the matches is used. This value is defaulted to 100000 amd cam be modified using <code>--posDiff</code>. Any matching pairs that are further than <code>--posDiff</code> are treated as unique to their files.

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	{{paramsParameter}}		{{paramsParameter}}

			{{PhoneHomeParameters}}

	~~= Usage =~~
	./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--all] [--flag] [--mapQual] [--mate] [--isize] [--seq] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--everyTag] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params]


	= Return Value =		= Return Value =

Mktrost at 03:19, 30 January 2013

2013-01-30T03:19:20Z

@@ Line 58: / Line 58: @@
 == input Files 1 & 2 (<code>--in1</code> and <code>--in2</code>)  ==
-Use <code>--in1</code> and <code>--in2</code> followed by your file names to specify the SAM/BAM input files to compare.
+Use <code>--in1</code> and <code>--in2</code> followed by your file names to specify the SAM/BAM input files to compare.  They are both required.
 The program automatically determines if your input files are SAM/BAM/uncompressed BAM unless your input file is stdin.
@@ Line 80: / Line 80: @@
 Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file).  This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported.
@@ Line 162: / Line 234: @@
 </pre>
-== SAM/Bam Format ==
+== SAM/BAM Format ==
 use .sam/.bam extension to output in SAM/BAM format instead of diff format.

Mktrost at 01:45, 30 January 2013

2013-01-30T01:45:34Z

@@ Line 11: / Line 11: @@
 By default, just the chromosome/position and cigar are compared for each record.
 Options are available to compare:
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 		--params      : print the parameter settings
 </pre>
 = Usage =
   ./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--all] [--flag] [--mapQual] [--mate] [--isize] [--seq] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--everyTag] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params]
 = Return Value =

Mktrost: /* SAM/Bam Format */

2012-05-21T17:55:45Z

SAM/Bam Format

← Older revision		Revision as of 17:55, 21 May 2012
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	# specified name with _only_<in1>.sam/bam with records only in the in1 file		# specified name with _only_<in1>.sam/bam with records only in the in1 file
	# specified name with _only_<in2>.sam/bam with records only in the in2 file		# specified name with _only_<in2>.sam/bam with records only in the in2 file

			Records that are identical in the two files are not written in any of these output files.

	When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:		When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:

Mktrost: /* SAM/Bam Format */

2012-05-21T17:27:34Z

SAM/Bam Format

← Older revision		Revision as of 17:27, 21 May 2012
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	When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:		When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:
	* ZF - Flag		* ZF - Flag
	* ZP - ~~Chrom/Pos~~		* ZP - Chromosome:1-based Position
	* ZC - Cigar		* ZC - Cigar
	* ZM - Mapping Quality		* ZM - Mapping Quality
	* ZN - Mate ~~chrom/pos~~		* ZN - Chromosome:1-based Mate Position
	* ZI - Insert Size		* ZI - Insert Size
	* ZS - Sequence		* ZS - Sequence

Mktrost: /* SAM/Bam Format */

2012-04-16T20:01:43Z

SAM/Bam Format

← Older revision		Revision as of 20:01, 16 April 2012
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	* ZQ - Base Quality		* ZQ - Base Quality
	* ZT - Tags		* ZT - Tags

			If <code>--onlyDiffs</code> is not specified, all fields that were compared will be printed in the tags. If <code>--onlyDiffs</code> is specified, then only the differing compared fields will be printed in the tags.

Mktrost at 18:44, 16 April 2012

2012-04-16T18:44:51Z

← Older revision		Revision as of 18:44, 16 April 2012
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	Options are available to compare:		Options are available to compare:
			* all fields
			* flags
			* mapping quality
			* mate chromosome/position
			* insert size
	* sequence		* sequence
	* base quality		* base quality
	* specified tags		* specified tags
			* all tags
	* turn off position comparison		* turn off position comparison
	* turn off cigar comparison		* turn off cigar comparison
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	Optional Parameters:		Optional Parameters:
	--out : output filename, use .bam extension to output in SAM/BAM format instead of diff format.		--out : output filename, use .bam extension to output in SAM/BAM format instead of diff format.
	In ~~SAMBAM~~ format there will be 3 output files:		In SAM/BAM format there will be 3 output files:
	1) the specified name with record diffs		1) the specified name with record diffs
	2) specified name with _only_<in1>.sam/bam with records only in the in1 file		2) specified name with _only_<in1>.sam/bam with records only in the in1 file
	3) specified name with _only_<in2>.sam/bam with records only in the in2 file		3) specified name with _only_<in2>.sam/bam with records only in the in2 file
			--all : diff all the SAM/BAM fields.
			--flag : diff the flags.
			--mapQual : diff the mapping qualities.
			--mate : diff the mate chrom/pos.
			--isize : diff the insert sizes.
	--seq : diff the sequence bases.		--seq : diff the sequence bases.
	--baseQual : diff the base qualities.		--baseQual : diff the base qualities.
	--tags : diff the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type...		--tags : diff the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type...
			--everyTag : diff all the Tags
	--noCigar : do not diff the the cigars.		--noCigar : do not diff the the cigars.
	--noPos : do not diff the positions.		--noPos : do not diff the positions.
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	= Usage =		= Usage =
	./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params]		./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--all] [--flag] [--mapQual] [--mate] [--isize] [--seq] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--everyTag] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params]

	= Return Value =		= Return Value =
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	The 3rd line (if a matching record was found) is the flag followed by the diff'd fields from the matching record.		The 3rd line (if a matching record was found) is the flag followed by the diff'd fields from the matching record.


	The diff'd record lines are tab separated, and are in the following order if --onlyDiffs is not specified:		The diff'd record lines are tab separated, and are in the following order if --onlyDiffs is not specified:
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	If <code>onlyDiffs</code> is specified, only the fields that are specified and are different get printed in lines 2 & 3.		If <code>onlyDiffs</code> is specified, only the fields that are specified and are different get printed in lines 2 & 3.

			If all fields are diffed and <code>--onlyDiffs</code> is specified, it may be difficult to determine which field is different.

	=== Example Output ===		=== Example Output ===
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	When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:		When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:
	* ZF - Flag		* ZF - Flag
	* ZP - Pos		* ZP - Chrom/Pos
	* ZC - Cigar		* ZC - Cigar
			* ZM - Mapping Quality
			* ZN - Mate chrom/pos
			* ZI - Insert Size
	* ZS - Sequence		* ZS - Sequence
	* ZQ - Base Quality		* ZQ - Base Quality
	* ZT - Tags		* ZT - Tags

Mktrost: /* Diff Format */

2012-04-16T18:02:33Z

Diff Format

@@ Line 71: / Line 71: @@
 The diff'd record lines are tab separated, and are in the following order if --onlyDiffs is not specified:
 * '<' or '>'
 * flag