C++ Class: SamRecord - Revision history

Ppwhite: /* Getting/Setting fields in a SAM/BAM Record */

2017-02-02T15:02:36Z

Getting/Setting fields in a SAM/BAM Record

← Older revision		Revision as of 11:02, 2 February 2017
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	The "get" accessors assume that the class has already been populated, either by using the set commands or by calling SamFile::ReadRecord. Not all of the values that can be retrieved using these get accessors have set methods. That is because they are either read from the file or are internally calculated values.		The "get" accessors assume that the class has already been populated, either by using the set commands or by calling SamFile::ReadRecord. Not all of the values that can be retrieved using these get accessors have set methods. That is because they are either read from the file or are internally calculated values.

	See: http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamFileHeader.html for documentation.		See: http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFileHeader.html for documentation.


	==Example of using getNextSamTag==		==Example of using getNextSamTag==

2011-09-06T20:49:36Z

Update to refer to doxygen

2010-11-17T20:18:46Z

2010-11-02T05:50:59Z

← Older revision		Revision as of 01:50, 2 November 2010
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	[[Category:~~libbam~~]]		[[Category:Software]]
			[[Category:C++]]
			[[Category:libStatGen]]
			[[Category:libStatGen BAM]]

	This class is part of [[C++ Library: ~~libbam\|libbam~~]].		This class is part of [[C++ Library: libStatGen]].

	== Setting fields in a SAM/BAM Record ==		== Setting fields in a SAM/BAM Record ==

2010-08-11T12:35:32Z

← Older revision		Revision as of 08:35, 11 August 2010
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	\| <code>const char* SamRecord::getQuality()</code>		\| <code>const char* SamRecord::getQuality()</code>
	\| Returns the SAM formatted Quality string.		\| Returns the SAM formatted Quality string.
			\|-
			\| <code>char SamRecord::getSequence(int index)</code>
			\| Get the sequence base at the specified index into this sequence, range: 0 to readLength - 1.
			\|-
			\| <code>char SamRecord::getQuality(int index)</code>
			\| Get the quality character at the specified index into this sequence, range: 0 to readLength - 1.
	\|-		\|-
	\|<code>Cigar* SamRecord::getCigarInfo()</code>		\|<code>Cigar* SamRecord::getCigarInfo()</code>

2010-08-11T12:32:50Z

@@ Line 177: / Line 177: @@
 | <code>const char* SamRecord::getQuality()</code>
 | Returns the SAM formatted Quality string.
 |-
 | <code>bool SamRecord::getFields(bamRecordStruct& recStruct, String& readName, String& cigar, String& sequence, String& quality)</code>

2010-06-03T14:11:48Z

← Older revision		Revision as of 10:11, 3 June 2010
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	\|-		\|-
	\| <code>bool SamRecord::getFields(bamRecordStruct& recStruct, String& readName, String& cigar, String& sequence, String& quality)</code>		\| <code>bool SamRecord::getFields(bamRecordStruct& recStruct, String& readName, String& cigar, String& sequence, String& quality)</code>
	\| Returns true if the passed in fields were successfully set, otherwise false. The bamRecordStruct that is set does not contain the values for the variable length fields. Tags are not returned by this method.		\| Returns true if the passed in fields were successfully set, otherwise false.
			The bamRecordStruct that is set does not contain the values for the variable length fields. Tags are not returned by this method.
	\|-		\|-
	\| <code>uint32_t SamRecord::getTagLength()>/code>		\| <code>uint32_t SamRecord::getTagLength()</code>
	\| Returns the length of the tags in BAM format.		\| Returns the length of the tags in BAM format.
	\|-		\|-

2010-06-03T14:10:58Z

← Older revision		Revision as of 10:10, 3 June 2010
Line 177:		Line 177:
	\| <code>const char* SamRecord::getQuality()</code>		\| <code>const char* SamRecord::getQuality()</code>
	\| Returns the SAM formatted Quality string.		\| Returns the SAM formatted Quality string.
			\|-
			\| <code>bool SamRecord::getFields(bamRecordStruct& recStruct, String& readName, String& cigar, String& sequence, String& quality)</code>
			\| Returns true if the passed in fields were successfully set, otherwise false. The bamRecordStruct that is set does not contain the values for the variable length fields. Tags are not returned by this method.
	\|-		\|-
	\| <code>uint32_t SamRecord::getTagLength()>/code>		\| <code>uint32_t SamRecord::getTagLength()>/code>

2010-06-01T21:57:33Z

← Older revision		Revision as of 17:57, 1 June 2010
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			[[Category:libbam]]

	This class is part of [[C++ Library: libbam\|libbam]].		This class is part of [[C++ Library: libbam\|libbam]].

2010-05-19T14:35:02Z

← Older revision		Revision as of 10:35, 19 May 2010
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	Returns true if successfully set, false if not.		Returns true if successfully set, false if not.
	\|-		\|-
	\| <code>bool SamRecord::setFlag(~~int16_t~~ flag)</code>		\| <code>bool SamRecord::setFlag(uint16_t flag)</code>
	\| Sets the bitwise FLAG to the passed in value.		\| Sets the bitwise FLAG to the passed in value.
	Returns true if successfully set, false if not.		Returns true if successfully set, false if not.
Line 119:		Line 119:
	\| Returns the length of the CIGAR in BAM format.		\| Returns the length of the CIGAR in BAM format.
	\|-		\|-
	\| <code>~~int16_t~~ SamRecord::getFlag()</code>		\| <code>uint16_t SamRecord::getFlag()</code>
	\| Returns the flag.		\| Returns the flag.
	\|-		\|-