BamUtil: squeeze - Revision history

Mktrost at 15:58, 26 March 2014

2014-03-26T15:58:44Z

Mktrost at 18:07, 6 January 2014

2014-01-06T18:07:26Z

← Older revision		Revision as of 18:07, 6 January 2014
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	--binHigh : Use the high end of the quality bin range for the quality value of the bin.		--binHigh : Use the high end of the quality bin range for the quality value of the bin.
	</pre>		</pre>
			{{PhoneHomeParamDesc}}

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

Mktrost at 15:40, 6 January 2014

2014-01-06T15:40:11Z

@@ Line 34: / Line 34: @@
                     but uses a lot of memory since it stores all the read names.
 		--rmTags     : Remove the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type...
 	Quality Binning Parameters (optional):
 	  Bin qualities by phred score, into the ranges specified by binQualS or binQualF (both cannot be used)
@@ Line 43: / Line 45: @@
 		--binMid     : Use the mid point of the quality bin range for the quality value of the bin.
 		--binHigh    : Use the high end of the quality bin range for the quality value of the bin.
 </pre>
+== Required Parameters ==
 {{inBAMInputFile}}
 {{outBAMOutputFile}}
 = Return Value =
-Returns the SamStatus for the reads/writes.
+Returns the SamStatus for the reads/writes (0 for success, non-0 for failure).

Mktrost: Update usage and start adding parameters

2011-10-07T21:35:23Z

Update usage and start adding parameters

← Older revision		Revision as of 21:35, 7 October 2011
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	= Overview of the <code>squeeze</code> function of <code>bamUtil</code> =		= Overview of the <code>squeeze</code> function of <code>bamUtil</code> =
	The <code>squeeze</code> option on the [[bamUtil]] executable reduces files size by optionally:		The <code>squeeze</code> option on the [[bamUtil]] executable reduces files size by optionally:
	* dropping OQ fields		* dropping OQ fields (default, disable using <code>--keepOQ</code>)
	* dropping duplicates		* dropping duplicates (default, disable using <code>--keepDups</code>)
	* dropping specified tags		* dropping specified tags (<code>--rmTags Tag1:Type1;Tag2:Type2</code>)
	* using '=' when a base matches the reference		* using '=' when a base matches the reference (<code>--refFile refFileName.fa</code>)
	* binning quality scores		* binning quality scores (<code>--binQualS</code><code>--binQualF</code>)
	* replacing readNames with unique integers		* replacing readNames with unique integers (<code>--readName</code>/<code>--sReadName</code>)


			= Usage =
			./bam squeeze --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <refFilePath/Name>] [--keepOQ] [--keepDups] [--readName <readNameMapFile.txt>] [--sReadName <readNameMapFile.txt>] [--binQualS <minQualBin2>,<minQualBin3><...>] [--binQualF <filename>] [--rmTags <Tag:Type[;Tag:Type]*>] [--noeof] [--params]


	= Parameters =		= Parameters =
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	</pre>		</pre>

	~~= Usage =~~
	./bam squeeze --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <refFilePath/Name>] [--keepOQ] [--keepDups] [--readName <readNameMapFile.txt>] [--sReadName <readNameMapFile.txt>] [--binQualS <minQualBin2>,<minQualBin3><...>] [--binQualF <filename>] [--rmTags <Tag:Type[;Tag:Type]*>] [--noeof] [--params]		{{inBAMInputFile}}
			{{outBAMOutputFile}}

Mktrost: /* Parameters */ Fix typo in usage

2011-09-27T17:19:18Z

Parameters: Fix typo in usage

← Older revision		Revision as of 17:19, 27 September 2011
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	--out : the SAM/BAM file to be written		--out : the SAM/BAM file to be written
	Optional Parameters:		Optional Parameters:
	--refFile : reference file name used to convert any bases that match the reference to '-'		--refFile : reference file name used to convert any bases that match the reference to '='
	--keepOQ : keep the OQ tag rather than removing it. Default is to remove it.		--keepOQ : keep the OQ tag rather than removing it. Default is to remove it.
	--keepDups : keep duplicates rather than removing records marked duplicate. Default is to remove them.		--keepDups : keep duplicates rather than removing records marked duplicate. Default is to remove them.
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	--params : print the parameter settings		--params : print the parameter settings
	</pre>		</pre>


	= Usage =		= Usage =

Mktrost: describe squeeze

2011-09-02T18:52:14Z

describe squeeze

New page

[[Category:BamUtil|squeeze]]
[[Category:BAM Software]]
[[Category:Software]]

= Overview of the <code>squeeze</code> function of <code>bamUtil</code> =
The <code>squeeze</code> option on the [[bamUtil]] executable reduces files size by optionally:
* dropping OQ fields
* dropping duplicates
* dropping specified tags
* using '=' when a base matches the reference
* binning quality scores
* replacing readNames with unique integers

= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
--out : the SAM/BAM file to be written
Optional Parameters:
--refFile : reference file name used to convert any bases that match the reference to '-'
--keepOQ : keep the OQ tag rather than removing it. Default is to remove it.
--keepDups : keep duplicates rather than removing records marked duplicate. Default is to remove them.
--sReadName : Replace read names with unique integers and write the mapping to the specified file.
This version requires the input file to have been presorted by readname, but
no validation is done to ensure this. If it is not sorted, a readname will
get mapped to multiple new values.
--readName : Replace read names with unique integers and write the mapping to the specified file.
This version does not require the input file to have been presorted by readname,
but uses a lot of memory since it stores all the read names.
--rmTags : Remove the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type...
Quality Binning Parameters (optional):
Bin qualities by phred score, into the ranges specified by binQualS or binQualF (both cannot be used)
Ranges are specified by comma separated minimum phred score for the bin, example: 1,17,20,30,40,50,70
The first bin always starts at 0, so does not need to be specified.
By default, the bin value is the low end of the range.
--binQualS : Bin the Qualities as specified (phred): minQualOfBin2, minQualofBin3...
--binQualF : Bin the Qualities based on the specified file
--binMid : Use the mid point of the quality bin range for the quality value of the bin.
--binHigh : Use the high end of the quality bin range for the quality value of the bin.
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
</pre>

= Usage =
./bam squeeze --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <refFilePath/Name>] [--keepOQ] [--keepDups] [--readName <readNameMapFile.txt>] [--sReadName <readNameMapFile.txt>] [--binQualS <minQualBin2>,<minQualBin3><...>] [--binQualF <filename>] [--rmTags <Tag:Type[;Tag:Type]*>] [--noeof] [--params]

= Return Value =
Returns the SamStatus for the reads/writes.

= Example Output =
<pre>
Number of records read = 13
Number of records written = 10
</pre>

← Older revision		Revision as of 15:58, 26 March 2014
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	* dropping OQ fields (default, disable using <code>--keepOQ</code>)		* dropping OQ fields (default, disable using <code>--keepOQ</code>)
	* dropping duplicates (default, disable using <code>--keepDups</code>)		* dropping duplicates (default, disable using <code>--keepDups</code>)
	* dropping specified tags (<code>--rmTags Tag1:Type1;Tag2:Type2</code>)		* dropping specified tags (<code>--rmTags "Tag1:Type1;Tag2:Type2"</code>)
	* using '=' when a base matches the reference (<code>--refFile refFileName.fa</code>)		* using '=' when a base matches the reference (<code>--refFile refFileName.fa</code>)
	* binning quality scores (<code>--binQualS</code><code>--binQualF</code>)		* binning quality scores (<code>--binQualS</code><code>--binQualF</code>)
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	= Usage =		= Usage =
	./bam squeeze --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <refFilePath/Name>] [--keepOQ] [--keepDups] [--readName <readNameMapFile.txt>] [--sReadName <readNameMapFile.txt>] [--binQualS <minQualBin2>,<minQualBin3><...>] [--binQualF <filename>] [--rmTags <Tag:Type[;Tag:Type]*>] [--noeof] [--params]		./bam squeeze --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <refFilePath/Name>] [--keepOQ] [--keepDups] [--readName <readNameMapFile.txt>] [--sReadName <readNameMapFile.txt>] [--binQualS <minQualBin2>,<minQualBin3><...>] [--binQualF <filename>] [--rmTags <"Tag:Type[;Tag:Type]*>"] [--noeof] [--params]


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	This version does not require the input file to have been presorted by readname,		This version does not require the input file to have been presorted by readname,
	but uses a lot of memory since it stores all the read names.		but uses a lot of memory since it stores all the read names.
	--rmTags : Remove the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type...		--rmTags : Remove the specified Tags formatted as "Tag:Type;Tag:Type;Tag:Type"...
	--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
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	=== Remove Tags (<code>--rmTags</code>) ===		=== Remove Tags (<code>--rmTags</code>) ===
	Use <code>--rmTags</code> followed by a list of tags separated by ';' to remove the specified tags. The tags should be formatted as: <code>Tag:Type"</code>		Use <code>--rmTags</code> followed by a list of tags separated by ';' to remove the specified tags. The tags should be formatted as: <code>"Tag:Type"</code>. Note: when using the ';' to specify multiple tags, be sure to put the whole string in quotes - otherwise the ';' will be interpreted as the end of the command. Example: <code>--rmTags "OQ:Z;MD:Z"</code> or <code>--rmTags 'OQ:Z;MD:Z'</code>

	{{noeofBGZFParameter}}		{{noeofBGZFParameter}}