C++ Class: SamFileHeader - Revision history

Ppwhite: /* Sam Header Basics */

2017-02-02T15:05:16Z

Sam Header Basics

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	=== Sam Header Basics ===		=== Sam Header Basics ===
	The SamFileHeader is comprised of multiple [http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecords].		The SamFileHeader is comprised of multiple [http://csg.sph.umich.edu//mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecords].

	There are 4 types of SAM Header Records:		There are 4 types of SAM Header Records:

2017-02-02T15:04:47Z

Sam Header Basics

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	The '''SamFileHeader''' also contains Comments, type CO. They are not included as part of the '''SamHeaderRecord''' class since they do not contain Tag/Value pairs.		The '''SamFileHeader''' also contains Comments, type CO. They are not included as part of the '''SamHeaderRecord''' class since they do not contain Tag/Value pairs.

	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.

	==== Additional Proposed Accessors ====		==== Additional Proposed Accessors ====

2011-08-24T22:05:42Z

2010-11-17T20:18:00Z

2010-11-02T05:50:17Z

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	[[Category:~~libbam~~]]		[[Category:Software]]
			[[Category:C++]]
			[[Category:libStatGen]]
			[[Category:libStatGen BAM]]

	== SamFileHeader ==		== SamFileHeader ==
	This class allows a user to get/set the fields in a SAM/BAM Header.		This class allows a user to get/set the fields in a SAM/BAM Header.

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

	=== Sam Header Basics ===		=== Sam Header Basics ===

2010-07-02T18:27:06Z

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	\|-		\|-
	\| <code>int SamFileHeader::GetReferenceID(const String & referenceName)</code>		\| <code>int SamFileHeader::GetReferenceID(const String & referenceName)</code>
			\| Returns the reference ID associated with the specified reference name (chromosome)
			\|-
			\| <code>int SamFileHeader::GetReferenceID(const char* referenceName)</code>
	\| Returns the reference ID associated with the specified reference name (chromosome)		\| Returns the reference ID associated with the specified reference name (chromosome)
	\|-		\|-

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	\|}		\|}

	==== Get a Specific Record ====		==== Get a Specific Header Record ====
	These methods return a reference to the specific record that was requested. They return NULL if that record does not exist in the header.		These methods return a reference to the specific record that was requested. They return NULL if that record does not exist in the header.

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	\| <code>const char* SamFileHeader::getSortOrder()</code>		\| <code>const char* SamFileHeader::getSortOrder()</code>
	\| Return the Sort Order value that is set in the Header. If this field does not exist, "" is returned.		\| Return the Sort Order value that is set in the Header. If this field does not exist, "" is returned.
			\|-
			\| <code>int SamFileHeader::GetReferenceID(const String & referenceName)</code>
			\| Returns the reference ID associated with the specified reference name (chromosome)
			\|-
			\| <code>const String& SamFileHeader::GetReferenceLabel(int id)</code>
			\| Returns the reference name (chromosome) associated with the specified reference ID.
	\|}		\|}

2010-07-02T11:45:47Z

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	! Method Name !! Description		! Method Name !! Description
	\|-		\|-
	\| <code>const char* SamFileHeader::~~getTagSO~~()</code>		\| <code>const char* SamFileHeader::getSortOrder()</code>
	\| Return the value ~~of the SO tag~~ in the ~~HD record~~. If ~~the~~ field does not exist, "~~unsorted~~" is returned.		\| Return the Sort Order value that is set in the Header. If this field does not exist, "" is returned.
	\|}		\|}

2010-07-01T18:00:32Z

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	NOTE: both getNextHeaderRecord and getNextHeaderLine increment the same iterator.		NOTE: both getNextHeaderRecord and getNextHeaderLine increment the same iterator.
	\|-		\|-
	\| <code>const char* SamFileHeader::getNextHeaderLine()</code>		\| <code>bool SamFileHeader::getNextHeaderLine(std::string& headerLine)</code>
	\| ~~Returns~~ the string ~~version of~~ the next header ~~record~~. ~~After all headers have been retrieved~~, "" ~~is returned~~ until a ~~reset~~ is called.		\| Set the passed in string to the next header line. The passed in string will be overwritten. If there are no more header lines or there is an error, false is returned and the passed in string is set to "" until a rest is called. Will also return the comment lines.
	~~Return~~ the comment lines.

	NOTE: both getNextHeaderRecord and getNextHeaderLine increment the same iterator.		NOTE: both getNextHeaderRecord and getNextHeaderLine increment the same iterator.

2010-07-01T15:48:40Z

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 | <code>void SamFileHeader::resetHeaderRecordIter()</code>
 | Resets to the beginning of the header records so the next call to getNextHeaderRecord/getNextHeaderLine returns the first header line.
 |}